Mercurial > repos > iuc > lofreq_filter

annotate test-data/indel-call-out.vcf @ 3:6b9548e15809 draft

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/tools/lofreq commit 0cec5f95ad0b141a9cc5be00be6d2574609b661a"
author iuc
date Fri, 29 May 2020 19:18:33 +0000
parents f4e8b08f26d4
children 08eab8cb7d14
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
f4e8b08f26d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"
iuc
parents:
diff changeset
1 ##fileformat=VCFv4.0
3
6b9548e15809 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 0cec5f95ad0b141a9cc5be00be6d2574609b661a"
iuc
parents: 2
diff changeset
2 ##fileDate=20200529
6b9548e15809 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 0cec5f95ad0b141a9cc5be00be6d2574609b661a"
iuc
parents: 2
diff changeset
3 ##source=lofreq call --verbose --ref reference.fa --call-indels --only-indels --sig 1 --bonf 1 --no-default-filter --no-default-filter -r pBR322:1-2180 -o /tmp/lofreq2_call_parallelafbznae0/0.vcf.gz reads.bam
2
f4e8b08f26d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"
iuc
parents:
diff changeset
4 ##reference=reference.fa
f4e8b08f26d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"
iuc
parents:
diff changeset
5 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
f4e8b08f26d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"
iuc
parents:
diff changeset
6 ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
f4e8b08f26d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"
iuc
parents:
diff changeset
7 ##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
f4e8b08f26d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"
iuc
parents:
diff changeset
8 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
f4e8b08f26d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"
iuc
parents:
diff changeset
9 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
f4e8b08f26d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"
iuc
parents:
diff changeset
10 ##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
f4e8b08f26d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"
iuc
parents:
diff changeset
11 ##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
f4e8b08f26d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"
iuc
parents:
diff changeset
12 #CHROM POS ID REF ALT QUAL FILTER INFO
3
6b9548e15809 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 0cec5f95ad0b141a9cc5be00be6d2574609b661a"
iuc
parents: 2
diff changeset
13 pBR322 725 . G GN 0 . ;HRUN=1
6b9548e15809 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 0cec5f95ad0b141a9cc5be00be6d2574609b661a"
iuc
parents: 2
diff changeset
14 pBR322 746 . A AN 0 . ;HRUN=1
6b9548e15809 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 0cec5f95ad0b141a9cc5be00be6d2574609b661a"
iuc
parents: 2
diff changeset
15 pBR322 747 . T TN 0 . ;HRUN=1
6b9548e15809 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 0cec5f95ad0b141a9cc5be00be6d2574609b661a"
iuc
parents: 2
diff changeset
16 pBR322 751 . G GN 0 . ;HRUN=1
6b9548e15809 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 0cec5f95ad0b141a9cc5be00be6d2574609b661a"
iuc
parents: 2
diff changeset
17 pBR322 807 . T TN 0 . ;HRUN=3
6b9548e15809 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 0cec5f95ad0b141a9cc5be00be6d2574609b661a"
iuc
parents: 2
diff changeset
18 pBR322 943 . C CCG 0 . ;HRUN=1
6b9548e15809 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 0cec5f95ad0b141a9cc5be00be6d2574609b661a"
iuc
parents: 2
diff changeset
19 pBR322 1152 . C CN 0 . ;HRUN=2
6b9548e15809 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 0cec5f95ad0b141a9cc5be00be6d2574609b661a"
iuc
parents: 2
diff changeset
20 pBR322 1271 . A AN 0 . ;HRUN=2
6b9548e15809 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 0cec5f95ad0b141a9cc5be00be6d2574609b661a"
iuc
parents: 2
diff changeset
21 pBR322 1376 . A ANN 0 . ;HRUN=1