How To Check If The Forward And Reverse Reads Have The Same Name In Bam File?
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11.7 years ago
Jordan ★ 1.3k

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 • 3.0k views
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11.7 years ago

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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I checked it manually. So they were the same.

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