Reference

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 2011-2024 (C) Erik Garrison and vcflib contributors. MIT licensed. Copyright 2020-2024 (C) Pjotr Prins.

AUTHORS

Erik Garrison and vcflib contributors.

History