Samtools and intrasample diversity

mstagliamonte · 07-23-2014, 08:19 AM

Hi, Seqanswers community,

I need some help with my variant calling.

I am dealing with a monocellular organisms, and I am expecting intrasample diversity due to multiclonality. This could mean that the real allele frequency is not necessarily 50% each (in case of biallelic snp)
After calling variants with samtools/bcftools, I would like to determine intrasample allele frequencies for each individual sample. Is there a way I can quantify the support for each allele with samtools (probably using the sam or bam files) or any similar program?

Hope what I've written makes sense, please let me know if you need any more information.

Thanks,
Max

swbarnes2 · 07-23-2014, 12:16 PM

I'd use samtools to make a pileup file, and then parse the line of the pileup for how many ref and alt letters you see.

mstagliamonte · 07-23-2014, 02:34 PM

Thanks, I'll try

Regards,
Max

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07-23-2014, 08:19 AM	#1
mstagliamonte Member Location: Florida Join Date: Feb 2013 Posts: 33	Samtools and intrasample diversity Hi, Seqanswers community, I need some help with my variant calling. I am dealing with a monocellular organisms, and I am expecting intrasample diversity due to multiclonality. This could mean that the real allele frequency is not necessarily 50% each (in case of biallelic snp) After calling variants with samtools/bcftools, I would like to determine intrasample allele frequencies for each individual sample. Is there a way I can quantify the support for each allele with samtools (probably using the sam or bam files) or any similar program? Hope what I've written makes sense, please let me know if you need any more information. Thanks, Max

07-23-2014, 12:16 PM	#2
swbarnes2 Senior Member Location: San Diego Join Date: May 2008 Posts: 912	I'd use samtools to make a pileup file, and then parse the line of the pileup for how many ref and alt letters you see.

07-23-2014, 02:34 PM	#3
mstagliamonte Member Location: Florida Join Date: Feb 2013 Posts: 33	Thanks, I'll try Regards, Max