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Old 08-06-2014, 03:43 PM   #3
spyf89
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Location: St. Louis

Join Date: Aug 2014
Posts: 2
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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, without the vcftools.pl varFilter step, there are SNPs called across all chromosomes. The information seems to be in order in the .bcf file...it's just not getting through the filtering step.

Thank you for the response!
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