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Forum: Bioinformatics 08-06-2014, 03:43 PM
Replies: 2
Views: 2,253
Posted By spyf89
I'll definitely check that out. I sorted the bam...

I'll definitely check that out. I sorted the bam to see if that fixed the problem (no luck) but perhaps they are sorted differently.

The only reason I think this might not fix things is because,...
Forum: Bioinformatics 08-06-2014, 12:31 PM
Replies: 2
Views: 2,253
Posted By spyf89
Missing chromosomes in vcf output

**UPDATE**

Problem solved. The local version of the .fai index file I was using only contained chromosome 1. Version on the server that I accidentally checked multiple times was fine. Whoops.
...
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