dsc-pileup takes forever to run

[aa9679]

Hi,

Even after all the filtering steps, the dsc-pileup step is taking forever to run. I wonder if it is because I am using a gvcf file, and the number of lines is 24901. Please let me know if you have any recommendations for how I can increase the speed of the run.

Thanks

[ghuls]

I think popscle is deprecated software for a while already as I didn't see any recent commits.

I now use cellsnp-lite (dsc-pileup replacement) and vireo (demuxlet and freemuxlet replacement) for the actual sample demultiplexing. cellsnp-lite is much faster than default dsc-pileup:

• https://github.com/single-cell-genetics/cellsnp-lite
• https://github.com/single-cell-genetics/vireo