Merging .gam files
1
0
Entering edit mode
18 months ago

Can anyone point me towards a method to merge gam files that are created by using ' vg map ' to map illumina reads to my genome graph? I would like to be able to map all of the sequencing runs separately and then merge the output (something like samtools merge but for a gam) so that I can call SVs for each sample.

Thanks.

vg gam • 628 views
ADD COMMENT
2
Entering edit mode
17 months ago
glenn.hickey ▴ 250

GAM files can be combined with cat. Note that vg call can only genotype one sample at a time, though.

ADD COMMENT
0
Entering edit mode

Hi Glenn,

Can you provide an example command on how to do this merge?

Thanks, ernesto

ADD REPLY

Login before adding your answer.

Traffic: 2723 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6