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

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!

bam
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updated by Ashutosh Pandey Ashutosh Pandey • written by Jordan Jordan

1 answer

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.

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written by Ashutosh Pandey Ashutosh Pandey

I checked it manually. So they were the same.

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written by Jordan Jordan

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