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Old 09-23-2013, 04:49 PM   #3
sophiespo
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Location: australia

Join Date: Apr 2013
Posts: 15
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Sorry to resurrect an old thread but I am also trying to figure this out.

samtools mpileup -DSuf ref.fa tumor.bam normal.bam | bcftools view -bvcgT pair - > var.bcf

This gives me mutations that are in both bam files. But I am only interested in mutations in the tumor and not the normal.

I have also performed separate analyses on each sample and then subtracted the normal from the tumor but this is not regarded as the best way to do things these days.

Ideas?
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