vcfparsealts

       Erik Garrison and vcflib contributors.

vcfparsealts (vcflib)                                                                            VCFPARSEALTS(1)

       Alternate allele parsing method.  This method uses pairwise alignment of REF and ALTs to determine compo‐
       nent allelic primitives for each alternate allele.

              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

0      Success

       not0  Failure

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

vcfparsealts

vcflib(1)

vcfparsealts