Off topic:Quickest Way To Pull A List Of Reads Out Of A Bam File?
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9.8 years ago

What is the quickest way find the final aligned locations of a list of reads in BAM file? I can call

samtools view my.bam | grep -e uniqueID1 -e uniqueID2 > output

to grep for uniqueID1 and uniqueID2 in my.bam, but crawling through the SAM is quite slow. I'd like to call:

handyTool extractID my.bam -l listOfIdentifiers > output

and get the SAM line for each identifier found in the BAM. Is there a better way?

samtools next-gen • 4.5k views
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