Rsamtools - Applypileups
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Entering edit mode
12.3 years ago
Donald • 0

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

samtools r pileup mpileup • 2.2k views
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Entering edit mode
12.3 years ago

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

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