search

single-cell-genetics / cellsnp-lite

Efficient genotyping bi-allelic SNPs on single cells
https://cellsnp-lite.readthedocs.io
Apache License 2.0
124 stars 11 forks source link

mode 1b query - #22

Closed bjstewart1 closed 2 years ago

bjstewart1 commented 2 years ago

when running in mode 1b

cellsnp-lite -S $BAM_list_file -i sample_list_file -O $OUT_DIR -R $REGION_VCF -p 20 --cellTAG None --UMItag None --gzip

I am trying to get genotype calls for a set of bulk RNAseq samples - each .bam passed to this corresponds to a separate donor, however the resulting vcf file doesn't produce genotype calls per-donor. Is this expected behaviour?

hxj5 commented 2 years ago

Hi, how about adding --genotype option and re-run

bjstewart1 commented 2 years ago

Yes this then produces cellSNP.cells.vcf.gz which has genotype calls for the individual bulk samples.

So this is the DONOR_GT_FILE file to pass to vireo? vireo -c $CELL_DATA -d $DONOR_GT_FILE -o $OUT_DIR

hxj5 commented 2 years ago

yes the file cellSNP.cells.vcf.gz can be used as DONOR_GT_FILE for vireo.

bjstewart1 commented 2 years ago

Terrific - thanks