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Old 03-26-2012, 12:19 PM   #1
swapnil2188
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Location: Indianapolis

Join Date: Feb 2012
Posts: 12
Default Samtools mpileup - Call somatic mutations from a pair of samples - detail steps ?

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 !
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