Call all types of SNP and Indels

Question

[2012201024]

HI, all,

I have a mapping BAM file, and want to use samtools software to call the all the SNP and Indels on every site, and each variation proportion on the site, if there are several variations on one site. I notice that the samtools can only output a few SNP and Indels under default parameters. I want to promote the VCF output more comprehensive. Can anyone tell me how to achieve this?

Many thanks in advance!

[Devon Ryan]

What do you mean by "each variation proportion on the site" and "promote the VCF output more comprehensive"? I assume the first one is, "report all possible variants with any support from the data" and the second is something like, "modify the VCF output to account for these multiple possible variants."

[2012201024]

Yeah, that is the exact I want to know. Sorry for poor English~~

Answer 1

[guillaume.rbt]

You can use the -B parameter using samtools mpileup, it disables BAQ computation and should be less sensitive.

(source: http://massgenomics.org/2012/03/5-things-to-know-about-samtools-mpileup.html)