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comparison test-data/samtools_mpileup_out_2.vcf @ 6:483949f5c3b0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author iuc
date Tue, 09 May 2017 11:15:58 -0400
parents da0203c3461a
children
comparison
equal deleted inserted replaced
5:9b8d98f0e6b2 6:483949f5c3b0
2 ##FILTER=<ID=PASS,Description="All filters passed"> 2 ##FILTER=<ID=PASS,Description="All filters passed">
3 ##samtoolsVersion=1.1+htslib-1.1 3 ##samtoolsVersion=1.1+htslib-1.1
4 ##samtoolsCommand=samtools mpileup --VCF --uncompressed -f /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_735.dat -g -e 20 -h 100 -L 250 -m 1 --open-prob 40 -F 0.002 -e 40 --output /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_736.dat /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_734.dat 4 ##samtoolsCommand=samtools mpileup --VCF --uncompressed -f /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_735.dat -g -e 20 -h 100 -L 250 -m 1 --open-prob 40 -F 0.002 -e 40 --output /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_736.dat /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_734.dat
5 ##reference=file:///tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_735.dat 5 ##reference=file:///tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_735.dat
6 ##contig=<ID=phiX174,length=5386> 6 ##contig=<ID=phiX174,length=5386>
7 ##ALT=<ID=X,Description="Represents allele(s) other than observed."> 7 ##ALT=<ID=*,Description="Represents allele(s) other than observed.">
8 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> 8 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
9 ##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel"> 9 ##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
10 ##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel"> 10 ##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
11 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> 11 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
12 ##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3"> 12 ##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
17 ##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric."> 17 ##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
18 ##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)"> 18 ##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
19 ##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h"> 19 ##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">
20 ##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling"> 20 ##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
21 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods"> 21 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
22 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_734.dat 22 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT localbam_0.bam