Mercurial > repos > iuc > lofreq_call

annotate test-data/call-out2.vcf @ 4:074d44697036 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 15:23:20 -0400
parents 31216d510164
children 65432c3abf6c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
1 ##fileformat=VCFv4.0
4
074d44697036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 0cec5f95ad0b141a9cc5be00be6d2574609b661a"
iuc
parents: 0
diff changeset
2 ##fileDate=20200529
074d44697036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 0cec5f95ad0b141a9cc5be00be6d2574609b661a"
iuc
parents: 0
diff changeset
3 ##source=lofreq call --verbose --ref reference.fa --sig 1 --bonf 1 --no-default-filter --no-default-filter -r pBR322:1-2180 -o /tmp/lofreq2_call_parallelkzkzyltj/0.vcf.gz reads.bam
0
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
4 ##reference=reference.fa
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
5 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
6 ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
7 ##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
9 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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).">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
11 ##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
12 #CHROM POS ID REF ALT QUAL FILTER INFO
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
13 pBR322 815 . A G 0 . DP=665;AF=0.003008;SB=6;DP4=333,311,0,2
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
14 pBR322 861 . A C 0 . DP=946;AF=0.002114;SB=3;DP4=447,497,0,2
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
15 pBR322 1001 . A C 0 . DP=1797;AF=0.000556;SB=3;DP4=877,918,1,0
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
16 pBR322 1013 . C G 0 . DP=1773;AF=0.000564;SB=0;DP4=875,897,0,1
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
17 pBR322 1068 . T G 0 . DP=1774;AF=0.000564;SB=3;DP4=853,920,1,0
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
18 pBR322 1084 . G T 0 . DP=1789;AF=0.000559;SB=3;DP4=875,913,1,0
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
19 pBR322 1113 . T A 0 . DP=1784;AF=0.000561;SB=0;DP4=885,898,0,1
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
20 pBR322 1134 . C T 49314 . DP=1767;AF=1.000000;SB=0;DP4=0,0,910,857
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
21 pBR322 1193 . G A 0 . DP=1698;AF=0.000589;SB=3;DP4=865,832,0,1
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
22 pBR322 1218 . A C 0 . DP=1708;AF=0.000585;SB=3;DP4=875,831,0,1
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
23 pBR322 1230 . T C 0 . DP=1759;AF=0.000569;SB=3;DP4=907,850,0,1
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
24 pBR322 1256 . A G 0 . DP=1746;AF=0.000573;SB=0;DP4=902,842,1,0
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
25 pBR322 1498 . C G 0 . DP=1195;AF=0.000837;SB=3;DP4=588,606,1,0
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
26 pBR322 1503 . T G 0 . DP=1156;AF=0.000865;SB=3;DP4=563,592,1,0
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
27 pBR322 1505 . G A 0 . DP=1137;AF=0.000880;SB=0;DP4=560,576,0,1