Question: Call all types of SNP and Indels
2
gravatar for 2012201024
6.0 years ago by
201220102420
China
201220102420 wrote:

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!

 

snp sequence alignment • 1.7k views
ADD COMMENTlink modified 6.0 years ago by guillaume.rbt830 • written 6.0 years ago by 201220102420

What do you mean by "each variation proportion on the site" and "promote the VCF output more comprenhensive"? 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."

ADD REPLYlink written 6.0 years ago by Devon Ryan98k

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

ADD REPLYlink modified 6.0 years ago • written 6.0 years ago by 201220102420
0
gravatar for guillaume.rbt
6.0 years ago by
guillaume.rbt830
France
guillaume.rbt830 wrote:

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 )

ADD COMMENTlink modified 6.0 years ago • written 6.0 years ago by guillaume.rbt830
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