bamdst
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shiquan
a lightweight bam file depth statistical tool
…paths(修复了outdir非绝对路径时多次创建的bug)
It's hard for me to figure out how to change the name of the output file with the current option. Do you have any good suggestions? Thanks!
Hi, when I use bamdst to stat WGS file, the output file depth.tsv.gz just has the first chrosome result in the region file, and the task is stoped with no...
like --cutoffdepth 500, 750, 1000 seems bamdst can only recognize the first number
bamdst is a good tools, but it has a bit problems. Raw Reads (All reads) is equal to the result of samtools view $bam | wc -l , not the...
Does bamdst remove duplicates reads automatically? I first used the "time picard MarkDuplicates REMOVE_DUPLICATES=true" function and calculate the coverage using "gatk DepthOfCoverage" based on removed duplicated bam file. The I...
hello, thanks for your Outstanding software， but I wander is there someway to accelerate the software？ I have about 1000 samples to do and why it can't support CRAM format
Hi @shiquan , I came across a warning when I make this software: ``` $ make make: Warning: File 'Makefile' has modification time 585 s in the future rm -fr...
Hi @shiquan Thanks for the great tool - I would suggest making this into a Bioconda recipe and having this installable/available via Bioconda - something similar to how csvtk is...
Can this program add support for multithreading to speed up analysis，The format is similar to --thread 4
