Mercurial > repos > iuc > snpsift

annotate test-data/extFields_test3_in.vcf @ 20:f90f08ed9810 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit df8a21df77acffe40c0bc0fe0409ca1b529cd7fc"
author iuc
date Sat, 11 Sep 2021 07:17:20 +0000
parents ede8954f5c82
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
17
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
1 ##fileformat=VCFv4.2
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
2 ##fileDate=20180328
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
3 ##source=freeBayes v1.1.0-46-g8d2b3a0-dirty
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
4 ##reference=localref.fa
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
5 ##contig=<ID=U00096,length=4639675>
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
6 ##phasing=none
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
7 ##commandline="freebayes --region U00096:0..4639675 --bam b_0.bam --bam b_1.bam --bam b_2.bam --bam b_3.bam --bam b_4.bam --bam b_5.bam --bam b_6.bam --bam b_7.bam --bam b_8.bam --bam b_9.bam --bam b_10.bam --bam b_11.bam --bam b_12.bam --fasta-reference localref.fa --vcf ./vcf_output/part_U00096:0..4639675.vcf --theta 0.001 --ploidy 1 -K -m 20 -q 20 -R 0 -Y 0 -e 1000 -F 0.2 -C 2 -G 1 --min-coverage 0 --min-alternate-qsum 0"
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
8 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
9 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
10 ##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
11 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
12 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
13 ##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
14 ##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
15 ##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
16 ##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
17 ##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
18 ##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
19 ##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
20 ##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
21 ##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
22 ##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
23 ##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
24 ##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
25 ##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
26 ##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
27 ##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
28 ##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
29 ##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
30 ##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
31 ##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
32 ##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
33 ##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
34 ##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
35 ##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
36 ##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
37 ##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without.">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
38 ##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
39 ##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout.">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
40 ##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
41 ##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing. Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
42 ##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
43 ##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
44 ##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
45 ##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
46 ##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
47 ##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
48 ##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
49 ##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
50 ##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record.">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
51 ##INFO=<ID=technology.ILLUMINA,Number=A,Type=Float,Description="Fraction of observations supporting the alternate observed in reads from ILLUMINA">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
52 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
53 ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
54 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
55 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
56 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
57 ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
58 ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
59 ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
60 ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
61 ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
62 ##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
63 ##SnpEffCmd="SnpEff -i vcf -o vcf -formatEff U00096 /galaxy-repl/main/files/024/679/dataset_24679041.dat "
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
64 ##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank | Genotype [ | ERRORS | WARNINGS ] )' ">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
65 ##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
66 ##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
67 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B C
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
68 U00096 1518079 . T G 1.82951E-13 . AB=0;ABP=0;AC=0;AF=0;AN=13;AO=13;CIGAR=1X;DP=170;DPB=170;DPRA=3.80208;EPP=7.18621;EPPR=80.8099;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=13;NUMALT=1;ODDS=31.1313;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=314;QR=4764;RO=157;RPL=9;RPP=7.18621;RPPR=8.0033;RPR=4;RUN=1;SAF=13;SAP=31.2394;SAR=0;SRF=63;SRP=16.3019;SRR=94;TYPE=snp;technology.ILLUMINA=1;EFF=synonymous_variant(LOW|SILENT|ggT/ggG|p.Gly343Gly/c.1029T>G|345|curA|protein_coding|CODING|b1449|1|G),upstream_gene_variant(MODIFIER||2861|c.-2861A>C|31|yncL|protein_coding|CODING|b4598||G),upstream_gene_variant(MODIFIER||1724|c.-1724A>C|149|ydcZ|protein_coding|CODING|b1447||G),upstream_gene_variant(MODIFIER||1209|c.-1209A>C|172|mnaT|protein_coding|CODING|b1448||G),upstream_gene_variant(MODIFIER||207|c.-207T>G|221|mcbR|protein_coding|CODING|b1450||G),upstream_gene_variant(MODIFIER||3252|c.-3252T>G|353|yncE|protein_coding|CODING|b1452||G),downstream_gene_variant(MODIFIER||4499|c.*4499T>G|264|ydcV|protein_coding|CODING|b1443||G),downstream_gene_variant(MODIFIER||3053|c.*3053T>G|474|patD|protein_coding|CODING|b1444||G),downstream_gene_variant(MODIFIER||2493|c.*2493T>G|57|ydcX|protein_coding|CODING|b1445||G),downstream_gene_variant(MODIFIER||2174|c.*2174T>G|77|ydcY|protein_coding|CODING|b1446||G),downstream_gene_variant(MODIFIER||908|c.*908A>C|700|yncD|protein_coding|CODING|b1451||G),downstream_gene_variant(MODIFIER||4426|c.*4426A>C|499|ansP|protein_coding|CODING|b1453||G) GT:DP:AD:RO:QR:AO:QA:GL 0:4:3,1:3:86:1:20:0,-6.02567 0:8:8,0:8:254:0:0:0,-23.1652 0:13:12,1:12:353:1:20:0,-30.048
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
69 U00096 1518212 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=13;AO=2;CIGAR=1X;DP=489;DPB=489;DPRA=0.250522;EPP=3.0103;EPPR=61.9789;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=13;NUMALT=1;ODDS=87.0721;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=78;QR=18812;RO=487;RPL=0;RPP=7.35324;RPPR=20.7076;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=285;SRP=33.7275;SRR=202;TYPE=snp;technology.ILLUMINA=1;EFF=upstream_gene_variant(MODIFIER||2994|c.-2994A>T|31|yncL|protein_coding|CODING|b4598||A),upstream_gene_variant(MODIFIER||1857|c.-1857A>T|149|ydcZ|protein_coding|CODING|b1447||A),upstream_gene_variant(MODIFIER||1342|c.-1342A>T|172|mnaT|protein_coding|CODING|b1448||A),upstream_gene_variant(MODIFIER||74|c.-74T>A|221|mcbR|protein_coding|CODING|b1450||A),upstream_gene_variant(MODIFIER||3119|c.-3119T>A|353|yncE|protein_coding|CODING|b1452||A),downstream_gene_variant(MODIFIER||4632|c.*4632T>A|264|ydcV|protein_coding|CODING|b1443||A),downstream_gene_variant(MODIFIER||3186|c.*3186T>A|474|patD|protein_coding|CODING|b1444||A),downstream_gene_variant(MODIFIER||2626|c.*2626T>A|57|ydcX|protein_coding|CODING|b1445||A),downstream_gene_variant(MODIFIER||2307|c.*2307T>A|77|ydcY|protein_coding|CODING|b1446||A),downstream_gene_variant(MODIFIER||124|c.*124T>A|345|curA|protein_coding|CODING|b1449||A),downstream_gene_variant(MODIFIER||775|c.*775A>T|700|yncD|protein_coding|CODING|b1451||A),downstream_gene_variant(MODIFIER||4293|c.*4293A>T|499|ansP|protein_coding|CODING|b1453||A),intergenic_region(MODIFIER|||n.1518212T>A|||||||A) GT:DP:AD:RO:QR:AO:QA:GL 0:10:8,2:8:312:2:78:0,-21.0397 0:9:9,0:9:356:0:0:0,-32.4019 0:65:65,0:65:2497:0:0:0,-224.912
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
70 U00096 1523784 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=13;AO=17;CIGAR=1X;DP=283;DPB=283;DPRA=2.07026;EPP=39.9253;EPPR=120.564;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=13;NUMALT=1;ODDS=63.7167;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=375;QR=9560;RO=266;RPL=0;RPP=39.9253;RPPR=6.9614;RPR=17;RUN=1;SAF=0;SAP=39.9253;SAR=17;SRF=189;SRP=105.412;SRR=77;TYPE=snp;technology.ILLUMINA=1;EFF=missense_variant(MODERATE|MISSENSE|tCg/tTg|p.Ser74Leu/c.221C>T|499|ansP|protein_coding|CODING|b1453|1|A),upstream_gene_variant(MODIFIER||2695|c.-2695C>T|700|yncD|protein_coding|CODING|b1451||A),upstream_gene_variant(MODIFIER||487|c.-487G>A|205|yncG|protein_coding|CODING|b1454||A),upstream_gene_variant(MODIFIER||1180|c.-1180G>A|70|yncH|protein_coding|CODING|b1455||A),upstream_gene_variant(MODIFIER||2142|c.-2142G>A|678|rhsE|protein_coding|CODING|b1456||A|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||4162|c.-4162G>A|160|ydcD|protein_coding|CODING|b1457||A),upstream_gene_variant(MODIFIER||4826|c.-4826G>A|350|yncI|protein_coding|CODING|b1459||A|WARNING_TRANSCRIPT_NO_START_CODON),downstream_gene_variant(MODIFIER||4833|c.*4833G>A|221|mcbR|protein_coding|CODING|b1450||A),downstream_gene_variant(MODIFIER||1392|c.*1392G>A|353|yncE|protein_coding|CODING|b1452||A) GT:DP:AD:RO:QR:AO:QA:GL 0:9:9,0:9:327:0:0:0,-29.7663 0:16:16,0:16:580:0:0:0,-52.5218 0:26:24,2:24:916:2:44:0,-78.566
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
71 U00096 1524994 . CTTT CT 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=13;AO=2;CIGAR=1M2D1M;DP=302;DPB=301;DPRA=0.368601;EPP=7.35324;EPPR=19.6872;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=13;NUMALT=1;ODDS=68.2413;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=71;QR=11356;RO=300;RPL=1;RPP=3.0103;RPPR=19.6872;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=170;SRP=14.5915;SRR=130;TYPE=del;technology.ILLUMINA=1;EFF=frameshift_variant(HIGH||ttc/|p.Phe12fs/c.34_35delTT|70|yncH|protein_coding|CODING|b1455|1|CT|INFO_REALIGN_3_PRIME),upstream_gene_variant(MODIFIER||3907|c.-3908_-3907delAA|700|yncD|protein_coding|CODING|b1451||CT),upstream_gene_variant(MODIFIER||992|c.-993_-992delAA|499|ansP|protein_coding|CODING|b1453||CT),upstream_gene_variant(MODIFIER||930|c.-930_-929delTT|678|rhsE|protein_coding|CODING|b1456||CT|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||2950|c.-2950_-2949delTT|160|ydcD|protein_coding|CODING|b1457||CT),upstream_gene_variant(MODIFIER||3614|c.-3614_-3613delTT|350|yncI|protein_coding|CODING|b1459||CT|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||4844|c.-4844_-4843delTT|378|ydcC|protein_coding|CODING|b1460||CT),downstream_gene_variant(MODIFIER||2604|c.*2604_*2605delTT|353|yncE|protein_coding|CODING|b1452||CT),downstream_gene_variant(MODIFIER||108|c.*108_*109delTT|205|yncG|protein_coding|CODING|b1454||CT);LOF=(yncH|b1455|1|1.00) GT:DP:AD:RO:QR:AO:QA:GL 0:6:6,0:6:209:0:0:0,-19.1481 0:9:7,2:7:271:2:71:0,-18.0127 0:26:26,0:26:1011:0:0:0,-91.2905
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
72 U00096 1525214 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=13;AO=2;CIGAR=1X;DP=325;DPB=325;DPRA=0.264151;EPP=3.0103;EPPR=21.8947;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=13;NUMALT=1;ODDS=54.1924;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=12493;RO=323;RPL=2;RPP=7.35324;RPPR=11.2458;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=153;SRP=4.9532;SRR=170;TYPE=snp;technology.ILLUMINA=1;EFF=upstream_gene_variant(MODIFIER||4125|c.-4125A>T|700|yncD|protein_coding|CODING|b1451||A),upstream_gene_variant(MODIFIER||1210|c.-1210A>T|499|ansP|protein_coding|CODING|b1453||A),upstream_gene_variant(MODIFIER||712|c.-712T>A|678|rhsE|protein_coding|CODING|b1456||A|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||2732|c.-2732T>A|160|ydcD|protein_coding|CODING|b1457||A),upstream_gene_variant(MODIFIER||3396|c.-3396T>A|350|yncI|protein_coding|CODING|b1459||A|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||4626|c.-4626T>A|378|ydcC|protein_coding|CODING|b1460||A),downstream_gene_variant(MODIFIER||2822|c.*2822T>A|353|yncE|protein_coding|CODING|b1452||A),downstream_gene_variant(MODIFIER||326|c.*326T>A|205|yncG|protein_coding|CODING|b1454||A),downstream_gene_variant(MODIFIER||38|c.*38T>A|70|yncH|protein_coding|CODING|b1455||A),intergenic_region(MODIFIER|||n.1525214T>A|||||||A) GT:DP:AD:RO:QR:AO:QA:GL 0:6:6,0:6:232:0:0:0,-21.246 0:11:11,0:11:433:0:0:0,-39.3229 0:38:38,0:38:1471:0:0:0,-132.652
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
73 U00096 1525377 . AGG AGGG,AGT 5.68956E-14 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=13;AO=2,3;CIGAR=1M1I2M,2M1X;DP=621;DPB=621.667;DPRA=0.196399,1.09363;EPP=3.0103,3.73412;EPPR=17.9768;GTI=0;LEN=1,1;MEANALT=2,1.5;MQM=60,60;MQMR=60;NS=13;NUMALT=2;ODDS=87.143;PAIRED=1,1;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=71,97;QR=23655;RO=613;RPL=2,1;RPP=7.35324,3.73412;RPPR=192.035;RPR=0,2;RUN=1,1;SAF=1,2;SAP=3.0103,3.73412;SAR=1,1;SRF=366;SRP=53.1738;SRR=247;TYPE=ins,snp;technology.ILLUMINA=1,1;EFF=upstream_gene_variant(MODIFIER||4290|c.-4290C>A|700|yncD|protein_coding|CODING|b1451||AGT),upstream_gene_variant(MODIFIER||4291|c.-4291_-4290insC|700|yncD|protein_coding|CODING|b1451||AGGG),upstream_gene_variant(MODIFIER||1375|c.-1375C>A|499|ansP|protein_coding|CODING|b1453||AGT),upstream_gene_variant(MODIFIER||1376|c.-1376_-1375insC|499|ansP|protein_coding|CODING|b1453||AGGG),upstream_gene_variant(MODIFIER||547|c.-547G>T|678|rhsE|protein_coding|CODING|b1456||AGT|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||546|c.-547_-546insG|678|rhsE|protein_coding|CODING|b1456||AGGG|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||2567|c.-2567G>T|160|ydcD|protein_coding|CODING|b1457||AGT),upstream_gene_variant(MODIFIER||2566|c.-2567_-2566insG|160|ydcD|protein_coding|CODING|b1457||AGGG),upstream_gene_variant(MODIFIER||3231|c.-3231G>T|350|yncI|protein_coding|CODING|b1459||AGT|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||3230|c.-3231_-3230insG|350|yncI|protein_coding|CODING|b1459||AGGG|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||4461|c.-4461G>T|378|ydcC|protein_coding|CODING|b1460||AGT),upstream_gene_variant(MODIFIER||4460|c.-4461_-4460insG|378|ydcC|protein_coding|CODING|b1460||AGGG),downstream_gene_variant(MODIFIER||2987|c.*2987G>T|353|yncE|protein_coding|CODING|b1452||AGT),downstream_gene_variant(MODIFIER||2988|c.*2987_*2988insG|353|yncE|protein_coding|CODING|b1452||AGGG),downstream_gene_variant(MODIFIER||491|c.*491G>T|205|yncG|protein_coding|CODING|b1454||AGT),downstream_gene_variant(MODIFIER||492|c.*491_*492insG|205|yncG|protein_coding|CODING|b1454||AGGG),downstream_gene_variant(MODIFIER||203|c.*203G>T|70|yncH|protein_coding|CODING|b1455||AGT),downstream_gene_variant(MODIFIER||204|c.*203_*204insG|70|yncH|protein_coding|CODING|b1455||AGGG),intergenic_region(MODIFIER|||n.1525379G>T|||||||AGT),intergenic_region(MODIFIER|||n.1525379_1525380insG|||||||AGGG) GT:DP:AD:RO:QR:AO:QA:GL 0:19:19,0,0:19:734:0,0:0,0:0,-66.383,-66.383 0:10:6,2,2:6:242:2,2:71,77:0,-15.396,-14.852 0:83:83,0,0:83:3242:0,0:0,0:0,-291.874,-291.874
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
74 U00096 1527079 . A G 7.60942E-10 . AB=0;ABP=0;AC=0;AF=0;AN=13;AO=2;CIGAR=1X;DP=67;DPB=67;DPRA=0.967742;EPP=7.35324;EPPR=8.65613;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=39.9846;NS=13;NUMALT=1;ODDS=22.6884;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=44;QR=2138;RO=65;RPL=2;RPP=7.35324;RPPR=7.05258;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=64;SRP=135.604;SRR=1;TYPE=snp;technology.ILLUMINA=1;EFF=missense_variant(MODERATE|MISSENSE|gAg/gGg|p.Glu385Gly/c.1154A>G|678|rhsE|protein_coding|CODING|b1456|1|G|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||3075|c.-3075T>C|499|ansP|protein_coding|CODING|b1453||G),upstream_gene_variant(MODIFIER||867|c.-867A>G|160|ydcD|protein_coding|CODING|b1457||G),upstream_gene_variant(MODIFIER||1531|c.-1531A>G|350|yncI|protein_coding|CODING|b1459||G|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||2761|c.-2761A>G|378|ydcC|protein_coding|CODING|b1460||G),upstream_gene_variant(MODIFIER||3997|c.-3997A>G|77|pptA|protein_coding|CODING|b1461||G),upstream_gene_variant(MODIFIER||4969|c.-4969A>G|281|nhoA|protein_coding|CODING|b1463||G),downstream_gene_variant(MODIFIER||4687|c.*4687A>G|353|yncE|protein_coding|CODING|b1452||G),downstream_gene_variant(MODIFIER||2191|c.*2191A>G|205|yncG|protein_coding|CODING|b1454||G),downstream_gene_variant(MODIFIER||1903|c.*1903A>G|70|yncH|protein_coding|CODING|b1455||G),downstream_gene_variant(MODIFIER||4227|c.*4227T>C|189|yddH|protein_coding|CODING|b1462||G) GT:DP:AD:RO:QR:AO:QA:GL 0:4:4,0:4:145:0:0:0,-12.7264 0:6:6,0:6:196:0:0:0,-17.3319 0:9:9,0:9:279:0:0:0,-24.5414
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
75 U00096 1527291 . G T 8.98077E-15 . AB=0;ABP=0;AC=0;AF=0;AN=13;AO=2;CIGAR=1X;DP=396;DPB=396;DPRA=0.215938;EPP=3.0103;EPPR=42.9311;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=13;NUMALT=1;ODDS=57.3966;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=13943;RO=393;RPL=0;RPP=7.35324;RPPR=39.2623;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=215;SRP=10.5745;SRR=178;TYPE=snp;technology.ILLUMINA=1;EFF=missense_variant(MODERATE|MISSENSE|Ggc/Tgc|p.Gly456Cys/c.1366G>T|678|rhsE|protein_coding|CODING|b1456|1|T|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||3287|c.-3287C>A|499|ansP|protein_coding|CODING|b1453||T),upstream_gene_variant(MODIFIER||655|c.-655G>T|160|ydcD|protein_coding|CODING|b1457||T),upstream_gene_variant(MODIFIER||1319|c.-1319G>T|350|yncI|protein_coding|CODING|b1459||T|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||2549|c.-2549G>T|378|ydcC|protein_coding|CODING|b1460||T),upstream_gene_variant(MODIFIER||3785|c.-3785G>T|77|pptA|protein_coding|CODING|b1461||T),upstream_gene_variant(MODIFIER||4757|c.-4757G>T|281|nhoA|protein_coding|CODING|b1463||T),downstream_gene_variant(MODIFIER||4899|c.*4899G>T|353|yncE|protein_coding|CODING|b1452||T),downstream_gene_variant(MODIFIER||2403|c.*2403G>T|205|yncG|protein_coding|CODING|b1454||T),downstream_gene_variant(MODIFIER||2115|c.*2115G>T|70|yncH|protein_coding|CODING|b1455||T),downstream_gene_variant(MODIFIER||4015|c.*4015C>A|189|yddH|protein_coding|CODING|b1462||T) GT:DP:AD:RO:QR:AO:QA:GL 0:12:12,0:12:422:0:0:0,-38.3029 0:12:12,0:12:418:0:0:0,-37.9417 0:48:48,0:48:1735:0:0:0,-156.391
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
76 U00096 1527328 . A C 5.89448E-14 . AB=0;ABP=0;AC=0;AF=0;AN=13;AO=53;CIGAR=1X;DP=371;DPB=371;DPRA=0;EPP=53.2;EPPR=17.4595;GTI=0;LEN=1;MEANALT=1;MQM=59.7547;MQMR=59.9843;NS=13;NUMALT=1;ODDS=49.8508;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=1375;QR=11600;RO=318;RPL=9;RPP=53.2;RPPR=3.44733;RPR=44;RUN=1;SAF=0;SAP=118.098;SAR=53;SRF=257;SRP=265.335;SRR=61;TYPE=snp;technology.ILLUMINA=1;EFF=missense_variant(MODERATE|MISSENSE|cAc/cCc|p.His468Pro/c.1403A>C|678|rhsE|protein_coding|CODING|b1456|1|C|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||3324|c.-3324T>G|499|ansP|protein_coding|CODING|b1453||C),upstream_gene_variant(MODIFIER||618|c.-618A>C|160|ydcD|protein_coding|CODING|b1457||C),upstream_gene_variant(MODIFIER||1282|c.-1282A>C|350|yncI|protein_coding|CODING|b1459||C|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||2512|c.-2512A>C|378|ydcC|protein_coding|CODING|b1460||C),upstream_gene_variant(MODIFIER||3748|c.-3748A>C|77|pptA|protein_coding|CODING|b1461||C),upstream_gene_variant(MODIFIER||4720|c.-4720A>C|281|nhoA|protein_coding|CODING|b1463||C),downstream_gene_variant(MODIFIER||4936|c.*4936A>C|353|yncE|protein_coding|CODING|b1452||C),downstream_gene_variant(MODIFIER||2440|c.*2440A>C|205|yncG|protein_coding|CODING|b1454||C),downstream_gene_variant(MODIFIER||2152|c.*2152A>C|70|yncH|protein_coding|CODING|b1455||C),downstream_gene_variant(MODIFIER||3978|c.*3978T>G|189|yddH|protein_coding|CODING|b1462||C) GT:DP:AD:RO:QR:AO:QA:GL 0:22:17,5:17:627:5:112:0,-46.4475 0:11:10,1:10:378:1:22:0,-32.1693 0:33:31,2:31:1151:2:49:0,-99.2161
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
77 U00096 1532370 . G T 7.50367E-15 . AB=0;ABP=0;AC=0;AF=0;AN=12;AO=2;CIGAR=1X;DP=378;DPB=378;DPRA=0.268293;EPP=3.0103;EPPR=19.9408;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=12;NUMALT=1;ODDS=74.0204;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=13838;RO=374;RPL=2;RPP=7.35324;RPPR=5.82044;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=216;SRP=22.5419;SRR=158;TYPE=snp;technology.ILLUMINA=1;EFF=missense_variant(MODERATE|MISSENSE|cGt/cTt|p.Arg108Leu/c.323G>T|281|nhoA|protein_coding|CODING|b1463|1|T),upstream_gene_variant(MODIFIER||495|c.-495C>A|189|yddH|protein_coding|CODING|b1462||T),downstream_gene_variant(MODIFIER||4408|c.*4408G>T|678|rhsE|protein_coding|CODING|b1456||T|WARNING_TRANSCRIPT_NO_START_CODON),downstream_gene_variant(MODIFIER||3942|c.*3942G>T|160|ydcD|protein_coding|CODING|b1457||T),downstream_gene_variant(MODIFIER||2707|c.*2707G>T|350|yncI|protein_coding|CODING|b1459||T|WARNING_TRANSCRIPT_NO_START_CODON),downstream_gene_variant(MODIFIER||1394|c.*1394G>T|378|ydcC|protein_coding|CODING|b1460||T),downstream_gene_variant(MODIFIER||1061|c.*1061G>T|77|pptA|protein_coding|CODING|b1461||T),downstream_gene_variant(MODIFIER||619|c.*619C>A|297|yddE|protein_coding|CODING|b1464||T),downstream_gene_variant(MODIFIER||1591|c.*1591C>A|226|narV|protein_coding|CODING|b1465||T),downstream_gene_variant(MODIFIER||2268|c.*2268C>A|231|narW|protein_coding|CODING|b1466||T),downstream_gene_variant(MODIFIER||2963|c.*2963C>A|514|narY|protein_coding|CODING|b1467||T),downstream_gene_variant(MODIFIER||4504|c.*4504C>A|1246|narZ|protein_coding|CODING|b1468||T) GT:DP:AD:RO:QR:AO:QA:GL 0:16:16,0:16:583:0:0:0,-52.8004 0:9:7,2:7:249:2:76:0,-15.539 0:46:46,0:46:1675:0:0:0,-151.009
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
78 U00096 1533613 . T C 6.56972E-15 . AB=0;ABP=0;AC=0;AF=0;AN=13;AO=2;CIGAR=1X;DP=489;DPB=489;DPRA=0.0989691;EPP=3.0103;EPPR=70.4686;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.9979;NS=13;NUMALT=1;ODDS=41.1942;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=80;QR=18551;RO=487;RPL=0;RPP=7.35324;RPPR=96.7582;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=203;SRP=32.265;SRR=284;TYPE=snp;technology.ILLUMINA=1;EFF=synonymous_variant(LOW|SILENT|ggA/ggG|p.Gly90Gly/c.270A>G|297|yddE|protein_coding|CODING|b1464|1|C),upstream_gene_variant(MODIFIER||1738|c.-1738A>G|189|yddH|protein_coding|CODING|b1462||C),downstream_gene_variant(MODIFIER||3950|c.*3950T>C|350|yncI|protein_coding|CODING|b1459||C|WARNING_TRANSCRIPT_NO_START_CODON),downstream_gene_variant(MODIFIER||2637|c.*2637T>C|378|ydcC|protein_coding|CODING|b1460||C),downstream_gene_variant(MODIFIER||2304|c.*2304T>C|77|pptA|protein_coding|CODING|b1461||C),downstream_gene_variant(MODIFIER||720|c.*720T>C|281|nhoA|protein_coding|CODING|b1463||C),downstream_gene_variant(MODIFIER||348|c.*348A>G|226|narV|protein_coding|CODING|b1465||C),downstream_gene_variant(MODIFIER||1025|c.*1025A>G|231|narW|protein_coding|CODING|b1466||C),downstream_gene_variant(MODIFIER||1720|c.*1720A>G|514|narY|protein_coding|CODING|b1467||C),downstream_gene_variant(MODIFIER||3261|c.*3261A>G|1246|narZ|protein_coding|CODING|b1468||C) GT:DP:AD:RO:QR:AO:QA:GL 0:26:26,0:26:1013:0:0:0,-91.465 0:11:11,0:11:417:0:0:0,-37.8758 0:58:58,0:58:2210:0:0:0,-199.104