How To Check If The Forward And Reverse Reads Have The Same Name In Bam File?

Question

[Jordan]

Hi,

I have a BAM file with paired reads. I'm using a tool to annotate SNPs and that tool needs the name of forward and reverse reads to be the same. How can I check if the BAM file has the same name for forward and reverse reads?

Thanks!

Answer 1

[Ashutosh Pandey]

I don't think you should worry about this. Most of the aligners trim the _1 and _2 string from the read name and thus both forward and reverse reads have the same name in BAM file. so go ahead with whatever you want to do.

[Jordan]

I checked it manually. So they were the same.