Extract Alignment By Read Id From A Sam File

Question

[Nicolas Rosewick]

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,

N.

[Pierre Lindenbaum]

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

[Pierre Lindenbaum]

duplicate of

Extracting subsets of reads from a BAM file

Answer 1

[Pierre Lindenbaum]

faster ?

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

[Aaronquinlan]

+1 for C locale.

[rob234king]

amazingly simple!!!! thanks so much

[rasha]

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

[GenoMax]

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