Question: Merging pe and contig alignments with Samtools
1
gravatar for zggayk
4.0 years ago by
zggayk10
United States
zggayk10 wrote:

 Does anyone know how to merge two BWA alignments into one using samtools? I have a pe read alignment and a contig alignment, both done with BWA and I was wondering how difficult it would be to merge these into one consensus alignment? 

The authors of the following paper (Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution)

did this with contigs and mate-pair reads: 

 

"The BAM format alignment files of the contig mapping and the mate-pair read mapping were subsequently merged using SAMtools suite v0.1.18  "

Zach

 

 

 

 

alignment • 1.2k views
ADD COMMENTlink written 4.0 years ago by zggayk10
1
gravatar for Ashutosh Pandey
4.0 years ago by
Philadelphia
Ashutosh Pandey11k wrote:

I am not sure if i have understood your question correctly but if you have aligned both contigs and mate-pair reads to the same reference genome, you can use samtools "merge" function to merge the two bam/alignment files. 

ADD COMMENTlink written 4.0 years ago by Ashutosh Pandey11k
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: 1243 users visited in the last hour