MAP QUALITY Filter Request

[haileye4]

Hey,

Our team has noticed our modkit extract calls output from aligned bams includes reads and CG sites where the MAPQ is 0.

So for example in this screenshot, you can see in IGV the bottom track has a CpG methylated site, but it's in all these reads with a map quality score of 0 (all reads that are completely white), so dorado was certain the alignment was wrong. We want to be able to extract all the calls but not those with a MAPQ of 0:

Looking through your documentation, it looks like there is no filter for MAPQ scores, is this something you could potentially add for us? In an aligned bam it's the 5th column, so I'm assuming it won't be hard to do. like --filter_mapq 10 or something and it could filter out all calls on a read with a MAPQ less than 10?

Thanks!

[ArtRand]

Hello @haileye4,

For extract calls you could filter MAPQ in samtools then pipe into Modkit like this:

samtools view -q $minq -h $bam \
  | modkit extract calls - filtered_extract_calls.tsv --no-filtering 

I agree that this would be a good feature to have for pileup, so I'll it to the list.