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single-cell-genetics / cellsnp-lite

Efficient genotyping bi-allelic SNPs on single cells
https://cellsnp-lite.readthedocs.io
Apache License 2.0
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cellsnp-lite runs indefinitely even on small BAM #24

Closed bradleycolquitt closed 2 years ago

bradleycolquitt commented 2 years ago

I have 10x multiome data that is a pool of 3 individuals from an outbred laboratory songbird population, and I'm interested in trying to demultiplex by individual.

When running cellsnp-lite on either the atac or gex bam files, the program runs seemingly indefinitely. This occurs even when running a small test bam containing only 200 records. The original cellSNP however processes this test bam quickly. This issue occurs both with the conda cellsnp-lite version and with a manually compiled version.

Here is the command I'm running:

/usr/local/bin/cellsnp-lite -s $BAM -b $BARCODE -O $OUT_DIR -p 22 \ --chrom NC_042576.1 \ --minMAF 0.1 \ --minCOUNT 100 \ --gzip \ --UMItag None

Not sure if this is relevant, but note that my chromosome identifiers are NCBI accession numbers and note UCSC standard "chr". Any thoughts on this? Thanks.

bradleycolquitt commented 2 years ago

I'm apparently too impatient. It looks to be running well.