I need to know if there is any read mapping to certain region in an alignment file (.sam). In fact, I have a list of 20 regions I'm interested. I'm talking about the third column in the sam file. Also, the reads I want to filter must map with an alignment score greater than a certain value.
I'm starting from 6 sam files.
Maybe a custom script is better than samtools?
1 answer
if there is any read mapping to certain region in an alignment file (.sam)
Also, the reads I want to filter must map with an alignment score greater than a certain value.
Please actually read the first link that Pierre posted. Grep should never be needed here.
Is this more or less what you suggested? 'specifics.locus' contains my interesting bed file first columns IDs that I'm trying to filter.
for file in *sam.bam.sorted.bam
do
bamToBed -i $file | awk -F"\t" '{if ($5 > 30) {print $0}}' > $file.bed
grep -x -f ./GBK/GBK_homologues/M6_f0_0taxa_algCOG_e0_/specifics.locus $file.bed &
done
BTW, this would be much faster if you made a sorted BAM file.
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