Find Mutations In A Region

Question

[Zhshqzyc]

Call mutations

How to call mutation within a region by comparing the sequences between tumor and normal samples of the same subject by using samtools?

TUMORBAM= the name of your tumor BAM file (ends in .bam) NORMALBAM= the name of your normal BAM file (ends in .bam)

Thanks.

[Jeremy Leipzig]

your other question was closer to the heart of the matter

Answer 1

[Sean Davis]

Samtools does not find somatic variants directly, though simply using mpileup will get you close. See, for example, varScan or somaticsniper as alternatives. There are several others that are not quite as well-documented. You could also write your own or use commercial software.

[Zhshqzyc]

I tried to use somaticsniper. However it seems to compare the entire region. How can I analyze a given region? I used the basic command:

somaticsniper -f [?] [?] [?] [?]

[Sean Davis]

Looks like somatic sniper does not have that option. You can always generate bam files of a specific region if you like using samtools view.