Question: Piping samtools merge to samtools calmd
0
gravatar for rubic
3.1 years ago by
rubic190
United States
rubic190 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 • 1.1k views
ADD COMMENTlink written 3.1 years ago by rubic190

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 3.1 years ago • written 3.1 years ago by Carlo Yague4.9k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 971 users visited in the last hour