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

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!

coverage bam alignment bedtools awk
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updated by ATpoint ATpoint • written by rimgubaev rimgubaev

2 answers 

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

Thank you, that works well!

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written by rimgubaev rimgubaev

A simple if does the trick.

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

Thanks, id is perfect!!!

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written by rimgubaev rimgubaev

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