Question: Merging pe and contig alignments with Samtools
gravatar for zggayk
4.0 years ago by
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  "






alignment • 1.2k views
ADD COMMENTlink written 4.0 years ago by zggayk10
gravatar for Ashutosh Pandey
4.0 years ago by
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
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