How do I summarize coverage across many genomes to inform filtering cutoffs?

Question

[selplat21]

Hello,

I used samtools depth to get a textfile of coverage across my genome for ~600 samples. In order to inform coverage cutoffs in the next step I'd like to make a summary/histogram of some sort that summarizes coverage for all of these genomes together.

For example, eventually I'd like to say, filter out reads below x coverage and above y coverage. This would be based on the distribution of coverage for all samples to filter out likely duplicates etc.

Any help is appreciated!

Answer 1

[onestop_data]

Please check this out Filter Bam File Based On Coverage and also take a look int the new samtools named coverage (samtools coverage). Please sure you have the latest samtools.

[selplat21]

Do you mean samtools stats --coverage? I only see this as a subcommand in the new samtools. This is very helpful thank you!

[onestop_data]

No. samtools coverage It was introduced here (samtools 1.10)