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Old 01-10-2014, 11:07 AM   #1
MU Informatics Research Core F
Location: Columbia, MO

Join Date: Oct 2010
Posts: 6
Default Samtools and bcftools: Why aren't some of the calls "missing data".

I'm using samtools mpileup and bcftools view to find variants. I'm perplexed why none of the alleles for any of the samples are shown as "missing data" (e.g. "./."). The coverage shouldn't be deep enough nor the samples similar enough for there not to be at least some "missing data". Here's my sample code:
samtools mpileup -uf ref.nfa A.bam B.bam C.bam  | bcftools view -vcg - > ABC.vcf
Is there a flag I'm missing or misusing?

This is using samtools version 0.1.19-44428cd and bcftools version 0.1.17-dev (r973:277) on CentOS 6.5 (64-bit).

Last edited by molecules; 01-10-2014 at 02:46 PM. Reason: Trying to fit code onto one line
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bam file, samtools bcftools, vcf file

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