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.\" Automatically generated by Pandoc 2.19.2
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.el \{\
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.TH "VCFPARSEALTS" "1" "" "vcfparsealts (vcflib)" "vcfparsealts (VCF statistics)"
.hy
.SH NAME
.PP
\f[B]vcfparsealts\f[R]
.SH SYNOPSIS
.PP
\f[B]vcfparsealts\f[R]
.SH DESCRIPTION
.PP
Alternate allele parsing method.
This method uses pairwise alignment of REF and ALTs to determine
component allelic primitives for each alternate allele.
.SH EXAMPLES
.IP
.nf
\f[C]
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
\f[R]
.fi
.SH EXIT VALUES
.TP
\f[B]0\f[R]
Success
.TP
\f[B]not 0\f[R]
Failure
.SH SEE ALSO
.PP
\f[B]vcflib\f[R](1)
.SH OTHER
.SH LICENSE
.PP
Copyright 2011-2024 (C) Erik Garrison and vcflib contributors.
MIT licensed.
Copyright 2020-2024 (C) Pjotr Prins.
.SH AUTHORS
Erik Garrison and vcflib contributors.
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