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Old 12-09-2011, 12:45 PM   #1
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Default Looking up specific position in bam


the problem is: I have a dataset consisting of multiple samples with called variations. If a variant is called in sample A, but not in sample B, I want to know if:

a) The sample agrees with the reference at that position
b) The site is not covered/not sufficiently covered

This is not quite trivial to script, and might be not the fastest solution.
Looking up using samtools tview is too tedious.
Is there a way to do that without scripting?
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Old 12-09-2011, 01:14 PM   #2
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samtools mpileup will take multiple bams, and either make side-by-side pileups, or side-by-side VCFs (though unfortunately some of the data is consolidated, and not split out by sample)

The multi-vcf is probably closer to what you want, as it will give you some kind of quality score for all the samples at any position where one of them shows a variant.
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Old 12-09-2011, 01:58 PM   #3
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Thanks, it's a start. In the long term, I want to use the GATK for calling and Annovar for annotating - then the called sets might be different.
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