Minimum Read Quality

[rishilpatel77]

Using the help option with python -m reditools -h, the default min_read_quality is stated to be 20. The output, however, still has the column "Coverage-q30", and the lowest MeanQ score for all editing events is 30 as well. Is the true default for min_read_quality actually 30 instead of 20 as stated in the manual? I also tried changing the -min-read-quality score to other values, such as 15 and 40, but the results were exactly the same as the default run. Is this the expected outcome?

[ahanden]

I think you're confusing "min-read-quality" with "min-base-quality".

min-read-quality filters by the MAPQ value in your bam file. I bet your alignment mostly has mapq values of 255 and some values below 10. You can see the distribution of mapq values with this code: samtools view [your_bam_file] | cut -f 5 | sort | uniq -c.

min-base-quality filters by the phred score of the base, which is what it sounds like you're looking for.

Interestingly, you did reveal a bug here. The Coverage-q30 column actually reports the coverage based on min-base-quality. I'll have to decide whether to update the column name or specifically report q30 coverage.