VCFPARSEALTS(1) vcfparsealts (VCF statistics) VCFPARSEALTS(1) NAME vcfparsealts SYNOPSIS vcfparsealts DESCRIPTION Alternate allele parsing method. This method uses pairwise alignment of REF and ALTs to determine component allelic primitives for each alternate allele. EXAMPLES Example: **vcfparsealts** samples/sample.vcf ##fileformat=VCFv4.0 (...) #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 ( A :: 111 A -> A; ) ( C :: 111 A -> C; ) 19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 ( A :: 112 A -> A; ) ( G :: 112 A -> G; ) 20 14370 rs6054257 G A 29 PASS AF=0.5;DP=14;NS=3;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. ( A :: 14370 G -> A; ) ( G :: 14370 G -> G; ) 20 17330 . T A 3 q10 AF=0.017;DP=11;NS=3 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. ( A :: 17330 T -> A; ) ( T :: 17330 T -> T; ) 20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;DP=10;NS=2;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. ( A :: 1110696 A -> A; ) ( G :: 1110696 A -> G; ) ( T :: 1110696 A -> T; ) 20 1230237 . T . 47 PASS AA=T;DP=13;NS=3 GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. ( . :: 1230237 T -> .; ) ( T :: 1230237 T -> T; ) 20 1234567 microsat1 G GA,GAC 50 PASS AA=G;AC=3,1;AN=6;DP=9;NS=3 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 ( G :: 1234567 G -> G; ) ( GA :: 1234567 G -> G; 1234568 -> A; ) ( GAC :: 1234567 G -> G; 1234568 -> AC; ) 20 1235237 . T . 0 . . GT 0/0 0|0 ./. ( . :: 1235237 T -> .; ) ( T :: 1235237 T -> T; ) X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 ( A :: 10 A -> A; 11 C -> ; ) ( AC :: 10 AC -> AC; ) ( ATG :: 10 A -> A; 11 -> T; 11 C -> G; ) Type: statistics EXIT VALUES 0 Success not 0 Failure SEE ALSO vcflib(1) OTHER LICENSE Copyright 2011-2025 (C) Erik Garrison and vcflib contributors. MIT li- censed. Copyright 2020-2025 (C) Pjotr Prins. AUTHORS Erik Garrison and vcflib contributors. vcfparsealts (vcflib) VCFPARSEALTS(1)
NAME | SYNOPSIS | DESCRIPTION | EXAMPLES | EXIT VALUES | SEE ALSO | OTHER | LICENSE | AUTHORS
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