How to calculate number of positions covered by at least 10 times in bam file?
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2.5 years ago
rimgubaev ▴ 280

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 • 507 views
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2.5 years ago
samtools depth in.bam | awk '($3>10)' | wc -l
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Thank you, that works well!

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2.5 years ago
ATpoint 65k

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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Thanks, id is perfect!!!

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