How to sub-sample .bam file to target coverage?

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3.3 years ago

hivemind ▴ 20

Hi,

I have .bam files for blood samples from which I extract signals. Let's assume my samples have a 30x coverage and my signal of interest is nicely detectable. To see how well the signal is detectable with lower coverage samples, I want to downsample to 20x, 10x, etc. Is there an easy way to do this?

So far I had a closer look at samtools view -s, but it takes only the target fraction and not a target coverage. Is there a program that lets me specify the target coverage that generalizes well for multiple samples with different start coverage?

QC downsample sequencing coverage • 1.4k views

ADD COMMENT • link 3.3 years ago by hivemind ▴ 20

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If you want to downsample from 30x to 20x then then just do samtools --subsample 0.66 .....

ADD REPLY • link 3.3 years ago by 4galaxy77 2.9k

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This assumes that unaligned reads are not in the BAM file? If they are then it may be best to filter those out first. someX coverage is a fluid term and subject to interpretation so it could mean different things to different people.

ADD REPLY • link 3.3 years ago by GenoMax 147k

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I know... If I had one sample or even five samples this would be my solution. I have hundreds of samples, all with different coverage and I was wondering whether there is a simpler solution that for example caps the max coverage to a certain value so that I don't have to calculate the fraction for each sample.

ADD REPLY • link 3.3 years ago by hivemind ▴ 20

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