Provided by: libvcflib-tools_1.0.9+dfsg1-2_amd64 bug

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 2011-2023 (C) Erik Garrison and vcflib contributors.  MIT licensed.

AUTHORS

       Erik Garrison and vcflib contributors.