Can I Merge The Good Quality (Unpaired Pe ) Bam File And Paired Pe Bam File With Samtools?

Question

[waswangs]

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

[Devon Ryan]

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

[Ashutosh Pandey]

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.

Answer 1

[Pavel Senin]

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