Galaxy | Tool Preview

VCFselectsamples: (version 1.0.0_rc3+galaxy0)

Allows to keep or remove samples from a VCF file.


Example:

Selecting NA00001 and NA00003 from the following VCF line:

#CHROM POS     ID        REF ALT QUAL FILTER INFO                              FORMAT      NA00001        NA00002      NA00003
20     1110696 rs6040355 A   G,T 67   PASS   NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,.

will, obviously, remove NA00002:

#CHROM POS     ID        REF ALT QUAL FILTER INFO                              FORMAT      NA00001        NA00003
20     1110696 rs6040355 A   G,T 67   PASS   NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2/2:35:4:.,.

Vcfselectsamples is based on vcfkeepsamples/vcfremovesamples utilities from VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).