Samtools mpileup - Call somatic mutations from a pair of samples - detail steps ?

[swapnil2188]

Can any one please clear some doubts regarding samtools mpileup - Call somatic mutations from a pair of samples ?

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

now I did get what each option means (DSuf...) but have doubts regarding others.

Now T stands for comparing two pair of samples for somatic variants but the syntax or the example command given only includes one.bam file.

Are we suppose to input two .bam files (files which need to be compared in order to find out somatic variants ?)

I used two bam files as input but it displays back the help menu again w/o any error been displayed. What can be the reason.

I have sorted and indexed the bam files (to be compared) already.
Is there something wrong with the command i used ?

What are the ideal steps to be followed for analysing somatic variants ?

Please can anyone help ?

Thanks !

[bpetersen]

I would also be interested in the exact steps to use for finding somatic mutations with samtools, any new insights yet?

[sophiespo]

Sorry to resurrect an old thread but I am also trying to figure this out.

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

This gives me mutations that are in both bam files. But I am only interested in mutations in the tumor and not the normal.

I have also performed separate analyses on each sample and then subtracted the normal from the tumor but this is not regarded as the best way to do things these days.

Ideas?