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brentp / mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

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.mosdepth.region.dist.txt missing values?

adamrtalbot opened this issue · comments

commented

I think this is expected behaviour or there might be a setting but I can't find how to change it.

The *.mosdepth.global.region.dist.txt and *.mosdepth.region.dist.txt are missing values between the integers. Tools like MultiQC then ignore these missing values, or treat as zero etc. For example: cat sample1.mosdepth.region.dist.txt | grep -e '^total' | tail -n 302 | head -3:

total   414     1.00
total   300     1.00
total   299     1.00

The missing values between 300 and 414 cause MultiQC to give this a coverage of 0. Obviously, it can be handled, but is there a setting just to export all values? I know the output will balloon in size but I'd rather retain data where possible.