Comments (4)
Hi, you can modify :
-F --flag <FLAG> exclude reads with any of the bits in FLAG set [default: 1796]
to exclude/include duplicates. By default they are excluded, you can include with:
-F 772
see more here: https://broadinstitute.github.io/picard/explain-flags.html
from mosdepth.
Thank you for your reply;
I have one more question. Can I get both results at the same time? Sequencing depth of raw data and deduplication sequencing depth
from mosdepth.
No, you'll have to run mosdepth twice.
from mosdepth.
thank you for your replay! have a nice day.
from mosdepth.
Related Issues (20)
- Fragment length filtering
- MAPQ 0 reads discarded even if --mapq 0 used HOT 2
- Empty per-base output file if all reads in input BAM are unmapped HOT 5
- Insert size of 0 HOT 1
- Can I get the two result at the same time?
- Summary output with --use-median
- Write out mean/median mapq HOT 1
- Report all chromosomes/regions even though they have zero coverage HOT 2
- Warnings about invalid chromosome intervals .
- Support for CRAM v3.1 HOT 5
- [question]: mosdepth 0.3.7 via bioconda/docker
- addition of min and max counts to prefix.regions.bed.gz
- Soft and hard clipped bases HOT 7
- Long run time with large assembly and many contigs HOT 9
- `:` in region strings passed to `--chrom`
- Unspecific naming of region in summary file HOT 2
- D4 support in versions 0.3.7 and 0.3.8 HOT 1
- feat: per base in BED regions only? HOT 3
- Differences in WES Coverage Values (Mosdepth Versions 0.3.3 and 0.3.8) HOT 2
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