Question: Piping samtools merge to samtools calmd
0
gravatar for rubic
23 months ago by
rubic180
United States
rubic180 wrote:

Hi,

Suppose I have 2 bam files: left.bam and right.bam that I want to merge and then pipe the outputed merged file to samtools calmd with a ref.fasta file. Will the appropriate command be:

samtools -n - left.bam right.bam | samtools calmd -b - ref.fasta
pipe samtools • 644 views
ADD COMMENTlink written 23 months ago by rubic180

You forgot the "merge" but other than that, I don't see anything wrong in that cmd. Does it work ?

samtools merge -n - left.bam right.bam | samtools calmd -b - ref.fasta
ADD REPLYlink modified 23 months ago • written 23 months ago by Carlo Yague4.4k
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