Hello,

another approach would be, to find "callable" regions in each of your bam file and intersect those region.

This can be done using mosdepth

export MOSDEPTH_Q0=NOT_CALLABLE
export MOSDEPTH_Q1=CALLABLE
mosdepth -n --quantize 0:20: sample1.quantized sample1.bam

This will give you a compressed bed. Regions with a coverage less then 20 are labeled as NOT_CALLABLE and those with greater or equal 20 as CALLABLE.

You can then extract only regions that are callable in this sample:

$ zgrep -w "CALLABLE" sample1.quantized.bed.gz|bgzip -c > sample1.callable.bed.gz

Repeat this for each sample. In the last step we intersect the callable region files to get a list of region which are callable in all of the files:

$ bedtools intersect -a sample1.callable.bed.gz -b sample2.callable.bed.gz sample3.callable.bed.gz ... > callable.bed

You can then use callable.bed in your downstream analysis to restrict the analysis to these regions.

fin swimmer

Maybe bedtools multicov is something to try. Do sliding windows coverage comparisons across multiple BAMs, then you'll identify regions with comparable coverage across all samples.

https://bedtools.readthedocs.io/en/latest/content/tools/multicov.html