cellsnp-lite
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Automatically detect all chromosomes in bam
Hi there, I ran cellsnp on my mouse data but ran into this error:
[W::check_args] Max depth set to maximum value (2147483647)
[I::main] mode 2b: pileup 22 whole chromosomes in 1 sample(s).
[E::csp_pileup] could not parse name for chrom 20.
[E::main] running mode 2b failed.
[E::main] Quiting...
[I::main] end time: 2022-10-27 23:59:26
[I::main] time spent: 0 seconds.
I just noticed that the default param for --chrom
is 1-22 however it's only 1-19 and M,X,Y in mouse, so if the default chromosomes could be automatically extracted from the input it'd be very much appreciated, thank you very much!
Also it'd be better to make the chromosome id be consistent between vcf and bam.., now it's like 1
in vcf but it's actually chr1
in bam
Oh nevermind if I set --chrom chr1 then in vcf it'll also be chr1, sorry I was just being dumb