Question: Piping samtools merge to samtools calmd
0
gravatar for rubic
18 months ago by
rubic170
United States
rubic170 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 • 499 views
ADD COMMENTlink written 18 months ago by rubic170

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 18 months ago • written 18 months ago by Carlo Yague4.2k
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: 909 users visited in the last hour