Experience Needed For Snp Calling By Samtools/Bcftools

Question

[C Shao]

Hi everyone:

I have successfully found some snps from whole exome data, mainly through samtools.

But I want to make a shorter list containing the more convincing snps. I guess read depth is important, what else should I consider?

I would like to hear your experience and suggestions. How did you select snps practically?

Besides, I used the default parameter to call snps, in which BAQ is enabled. In may case the coverage is around 25X. Should I use -E or -S instead to find more snps? How you usually use samtools to find snps?

Thanks.

Answer 1

[Zev.Kronenberg]

Browse these links:

http://www.biostars.org/post/show/48781/best-practices-faster-samtools-mpileup-any-tips/

and

http://biostar.stackexchange.com/post/show/1268/what-is-the-best-pipeline-for-human-whole-exome-sequencing/

and

http://seqanswers.com/forums/archive/index.php/t-6576.html

and

http://samtools.sourceforge.net/mpileup.shtml