Rsamtools - Applypileups

Question

[Donald]

I am trying to get the equivalent of : samtools mpileup -f reference.fa reads.bam

but in R. I can't find where and how to add the reference sequence into the function call?

Cheers

Answer 1

[Sukhi Singh]

Hey, I also checked for it, I think the best would to invoke a system call within R calling samtools pileup and then parsing the data back for the time being.

system('samtools mpileup -f reference.fa reads.bam')

Cheers