Question: Can I Merge The Good Quality (Unpaired Pe ) Bam File And Paired Pe Bam File With Samtools?
0
gravatar for waswangs
6.7 years ago by
waswangs0
Beijing, China
waswangs0 wrote:

Hi there, I filtered my PE reads based on strict parameters, but now i want to make good use of the good quality (unpaired PE) reads. What i should do? the unpaired PE and paired PE have been mapped to the reference genome and been converted to BAM files. Can i merge them by samtools? Thanks

illumina bam samtools • 2.7k views
ADD COMMENTlink modified 6.7 years ago by Pavel Senin1.9k • written 6.7 years ago by waswangs0

You can do whatever you want. Whether you should or not is dependent upon what you need to do with the data downstream.

ADD REPLYlink written 6.7 years ago by Devon Ryan96k

I am just adding to what dpryan79 said. It really depends on what you want to do with your bam file. For most of the downstream analysis including callings SNPs and small Indels, you can use read which itself is mapped with high mapping quality (or uniquely mapped) but its pair couldn't be mapped because of some reason. Its important to include such reads in case your objective is to call for structural variants. Some SV callers make use of unmapped read of the read pair where other read is mapped to identify deleted regions.

ADD REPLYlink written 6.7 years ago by Ashutosh Pandey12k
0
gravatar for Pavel Senin
6.7 years ago by
Pavel Senin1.9k
Los Alamos, NM
Pavel Senin1.9k wrote:

I think that it is safe to merge paired and unpaired alignments. According to SAM flags, reads can be paired and unpaired.

ADD COMMENTlink modified 6.7 years ago • written 6.7 years ago by Pavel Senin1.9k
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: 1180 users visited in the last hour