How to calculate number of positions covered by at least 10 times in bam file?

Question

[rimgubaev]

Hello everyone! I wonder if somebody could recommend how to calculate the number of positions covered by at least 10 times in bam file? To calculate the number of positions covered by at least once in the bam file I used this oneliner:

bedtools genomecov -ibam my_alignment.bam -bg | awk '{ s+=($3-$2) } END { print s }'

But I have no idea how to modify it, so please help!

Answer 1

[Pierre Lindenbaum]

samtools depth in.bam | awk '($3>10)' | wc -l

[rimgubaev]

Thank you, that works well!

Answer 2

[ATpoint]

A simple if does the trick.

bedtools genomecov -ibam my_alignment.bam -bg | awk '{ if($4 >= 10) s+=($3-$2) } END { print s }' foo

[rimgubaev]

Thanks, id is perfect!!!