Extract Alignment By Read Id From A Sam File

Hi,

Is there a rapid way to extract alignment from a sam file using read ids (about~100 read ids in average). If the read ids are in a file (one per line), I could do :

cat in.sam | grep -f idFile.txt > out.sam

but with a big sam file (~40Gb) it takes a lot of time.... so is there maybe a method to extract these alignments faster ?

Thanks,

sam read id

• 13,944 views • link

updated 13.3 years ago by Pierre Lindenbaum

• written 13.3 years ago by Nicolas Rosewick

duplicate of

Extracting subsets of reads from a BAM file

• 0 views • link

written 13.3 years ago by Pierre Lindenbaum

well, not really duplicate. It was BAM, not SAM.

• 0 views • link

written 13.3 years ago by Pierre Lindenbaum

1 answer

faster ?

 LC_ALL=C grep -w -F -f idFile.txt  < in.sam > subset.sam

• 180 views • link

written 13.3 years ago by Pierre Lindenbaum

+1 for C locale.

• 0 views • link

written 13.3 years ago by Aaronquinlan

amazingly simple!!!! thanks so much

• 0 views • link

written 12.6 years ago by rob234king

thanks so much for this! any suggestion on how to also keep the sam header in the output subset.sam file?

• 1 views • link

written 8.1 years ago by rasha •

Capture the header (Lines starting with ^@). Add to the new subset.sam file.

• 1 views • link

written 8.1 years ago by GenoMax

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