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Old 09-06-2012, 01:46 AM   #2
AWeller
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Location: Germany

Join Date: Feb 2011
Posts: 4
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I'm not sure if I understand your question correctly.

In general, omitting the "-v" in bcftools will show you all positions, not just the variants.

A convenient way to manually inspect a single position that didn't get called is the "samtools mpileup -r" option, where eg "samtools mpileup -r CHROMOSOMEII:10-10 ..." will show you only this one location.

If you are talking about doing this in bulk for the whole genome, a possibility is to do a second pileup of all positions and then find the differences via "diff" or a custom script.

Hope to help,

best
Andreas
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