mosdepth
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brentp
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
Hi, I am running into an issue related to d4 when trying build the latest mosdepth release: ``` #35 158.2 CC: ../../../../root/.nimble/pkgs/d4-0.0.3/d4pkg/d4_sys.nim #35 158.2 CC: ../../../../root/.nimble/pkgs/d4-0.0.3/d4.nim #35 158.3 CC: mosdepth.nim...
When processing large numbers of samples and storing the results for systematic comparisons it's handy to store results even for uncovered contigs. The .mosdeth.summary.txt file currently omits uncovered contigs. While...
I've calculated mosdepth coverage with the command: mosdepth -n -b 500 -x -t 4 -Q30 $OUTPUT_DIR/${base%.cov} ${this_bam} I run plot-dist.py with: python mosdepth-0.3.3/scripts/plot-dist.py *.global.dist.txt However, the output prints to screen...
Hi all I was hoping to find help here. I am doing some ATAC_Seq analysis. I am trying to compare peak callers Genrich (atac-seq specific) and MACS2 for the same...
Hi, Given that mosdepth can be installed from source with independent htslib, and htslib supports streaming from cloud storage buckets, I'm wondering how difficult it would be, for mosdepth to...
#174 sorry for a new issue here, because I can not comment at a close issue. threshold output to indicate how many bases in each region are covered at the...
When running mosdepth with a bed input file of regions, the regions get sorted in the output file. What is the exact sorting command used? I would like to reproduce...
You indicated you where willing to accept a PR for changing the behaviour of mosdepth so that it does not remove content present in input bed region file, I am...
I align my reads against a genome with >232k scaffolds, but am only interested in coverage reports of a few of these scaffolds, and this causes mosdepth to eventually being...
Hi, I have a Macbook Pro 2021 M1, Macos 12.2.1 (21D62) and get this error "zsh: exec format error: mosdepth", when I execute mosdepth installed via conda. Going to previous...
