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barkasn / scAlleleCount

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Extremely long run time #2

Open chrisamiller opened 6 years ago

chrisamiller commented 6 years ago

I'm running the following command on a single site, and it's still running 7 hours later. Is this expected? 

reading snps file... done
building positions index... done
reading barcodes file... reading barcodes file... done
building barcodes index... done
perfoming pileup........................................................................................................................................................................................................................................................

Is it doing pileup for the entire bam, rather than just the single needed site?

saralinker commented 1 year ago

I see that the issue is still open but was wondering if you @chrisamiller resolved this on your own? I'm coming across the same issue.

chrisamiller commented 1 year ago

We ended up building our own tool (https://github.com/sridnona/cb_sniffer), and also working in collaboration with 10x to build another (https://github.com/10XGenomics/vartrix). I'd recommend giving one of them a shot instead.

saralinker commented 1 year ago

Thanks for the reply @chrisamiller I'm still running into issues and am doing it "by hand" (splitting bams and running freebayes) currently. I'll check out vartrix and cb_sniffer.

edit: for anyone else coming across this, cb_sniffer is performing really well, vartrix has some additional bugs.