brentp / mosdepth

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

brentp/mosdepth Issues

Long run time with large assembly and many contigs
Closed 23 days ago9
Soft and hard clipped bases
Closed a month ago7
Build failure with nim 2.0.0
Updated a month ago3
addition of min and max counts to prefix.regions.bed.gz
Updated a month ago
[question]: mosdepth 0.3.7 via bioconda/docker
Updated 2 months ago
Support for CRAM v3.1
Closed 2 months ago5
Warnings about invalid chromosome intervals .
Updated 3 months ago
Report all chromosomes/regions even though they have zero coverage
Updated 3 months ago2
Write out mean/median mapq
Closed 4 months ago1
misleading output in `summary.txt` file
Updated 4 months ago3
Summary output with --use-median
Updated 4 months ago
sequencing depth after deduplication
Closed 4 months ago4
Can I get the two result at the same time?
Closed 4 months ago
Insert size of 0
Updated 5 months ago1
Empty per-base output file if all reads in input BAM are unmapped
Closed 6 months ago5
Fragment length filtering
Closed 6 months ago
MAPQ 0 reads discarded even if --mapq 0 used
Closed 6 months ago2
[Question]: mosdepth 0.3.5 in bioconda/docker
Closed 7 months ago2
--d4 option unavailble in 0.3.4
Closed 7 months ago3
Filtering alignments: -F in which format?
Closed 7 months ago1
funny global depth of coverage plot
Updated 8 months ago1
Wrong calculation of minimum coverage?
Closed 8 months ago8
very high panel sequencing depth issue - difference depth output in mosdepth depth, bedtools coverage, and sambamba output
Updated 8 months ago1
testrun for region chr1:1000-2000 takes ages
Updated 9 months ago2
question about WGS data
Closed 9 months ago1
[Question]: mosdepth 0.3.4 via Docker or Conda
Updated 9 months ago2
--by capture.bed still give out region not in bed
Closed 10 months ago6
how coverage in region is calculated
Closed a year ago1
equivalent to genomeCoverageBed
Closed a year ago1
Version? 0.3.4?
Closed a year ago1
issue with bed file
Closed a year ago1
High memory usage for very small BAM files
Closed a year ago1
specific chromosome list for mosdepth running
Closed a year ago2
"SIGSEGV: Illegal storage access. (Attempt to read from nil?)" when using bed file
Closed a year ago5
Percentage of Coverage for Exome Bed file
Updated a year ago1
[hts-nim] error adding to csi index
Closed a year ago4
Exclusion of reads with -F flag
Closed a year ago2
Coverage by region vs. Global dist
Updated a year ago8
question: `--by` and quantized output
Closed a year ago2
depth per strand
Closed a year ago1
`REF_PATH` differs from samtools behaviour
Closed a year ago1
.mosdepth.region.dist.txt missing values?
Updated a year ago
Support for streaming
Closed a year ago1
In summary.txt what's the difference between length and bases?
Updated a year ago
compute best sliding window coverage per chromosome
Closed 2 years ago1
Error building 0.3.3
Updated 2 years ago1
Optionally report uncovered contigs in summary file
Updated 2 years ago
difference in X-Coverage calculated by Mosdepth and Samtools Coverage
Closed 2 years ago2
plot.dist.py output to screen only
Updated 2 years ago4
sorting issue
Updated 2 years ago1