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Old 04-05-2012, 10:08 AM   #1
Location: Indianapolis

Join Date: Feb 2012
Posts: 12
Default Doubts regarding samtools mpileup - Call somatic mutations from a pair of samples ?

I am trying to compare two samples for somatic mutations using Samtools mpileup. (RNAseq data)

The two .bam files or samples I am comparing include multiple samples merged together into them (3 .bam files in one and 8 in other- merged using samtools merge)

The command given in the manual
( " samtools mpileup -DSuf ref.fa aln.bam | bcftools view -bvcgT pair - > var.bcf" ) doesnt specify the number of samples (inputs)

I used this command

samtools mpileup -DSuf ref.fa aln1.bam aln2.bam | bcftools view -bvcgT pair - > var.bcf

It gives me back the error saying
"[mpileup] 1 samples in 2 input files
<mpileup> Set max per-file depth to 8000
[afs] 0:0.000"

I also tried to make a sample.txt file for the two samples (merged files) and used this command

"samtools mpileup -DSuf ref.fa aln1.bam aln2.bam | bcftools view -bvcgT pair -s samples.txt - > var.bcf "

I still get an error (different error)

Is there anything wrong here ?

What should be the ideal steps to find out somatic variants between two samples ? (samples include multiple bam files merged together)

Please suggest me some steps to be followed in order to find out somatic variants by comparing two samples using samtools mpileup

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