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brentp
Add in min read length threshold?
Hi mosdepth peeps,
Just wondering if it would be possible to add in a feature from samtools depth to this tool.
Specifically, something like samtools depth -l 5000
-l <int> read length threshold (ignore reads shorter than <int>) [0]
We are working with Nanopore reads and are wanting to look at coverage using only reads that are >10kb, which is what we used for our de novo assembly. (Yes we could trim our raw fast files but this is a pretty time intensive step with the current tools).
Cheers and thanks! Megan
This is pretty easy to implement. Would like to get others to weigh in on how broadly useful this is. Is this something that's commonly needed for long-read data?
cc @wdecoster
It's not something that I personally have needed already - but I can see some value in it. I can imagine that you want to know the coverage obtained from the "informative/useful" alignments, discarding the reads that were not optimal for assembly or SV calling.
Yes, we assemble de novo primarily with Canu, which has a minimum read cut-off, so it just discards reads shorter than X before going into the k-mer counts and overlaps to generate error corrected reads. I was aligning Canu "trimmed" or "corrected" reads back to my genome but it has been suggested (I forget where I read/heard this) that we really should use the raw data to do this, not the Canu modified reads.
We are interested in exactly what @wdecoster mentions, a SV that seems to be moving around between chromosomes. And we are trying to assess if this is a gross mis-assembly or something real by looking at the genome coverage around this region.
Thanks very much for considering!
@brentp Related to this, I'm working on cell-free DNA, where tumor-derived DNA fragments tend to be shorter than the blood-related fragments. I would like to test if measuring the coverage separately for <150bp and >150bp would give me better results. I could subset my bam files prior to using mosdepth, but it would be great if I could simply set fragment length filters in the mosdepth call. Would this be possible?
