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

lose cellSNP.cells.vcf.gz file #4

Closed penglbio closed 3 years ago

penglbio commented 3 years ago

When I test the software cellSNP-lite and cellSNP, I find the output files of cellSNP-lite have no cellSNP.cells.vcf.gz file. The following is my command: cellsnp-lite -s demux.B.lite.bam -b demux.B.barcodes.400.tsv -O test1 -p 22 --minMAF 0.1 --minCOUNT 100 --gzip

cellSNP.base.vcf.gz cellSNP.samples.tsv cellSNP.tag.AD.mtx cellSNP.tag.DP.mtx cellSNP.tag.OTH.mtx

cellSNP -s demux.B.lite.bam -b demux.B.barcodes.400.tsv -O test2 -p 22 --minMAF 0.1 --minCOUNT 100

6 output files: cellSNP.base.vcf.gz cellSNP.cells.vcf.gz cellSNP.samples.tsv cellSNP.tag.AD.mtx cellSNP.tag.DP.mtx cellSNP.tag.OTH.mtx

hxj5 commented 3 years ago

Hi, you could add --genotype option for cellsnp-lite so that it will output cellSNP.cells.vcf.gz

huangyh09 commented 3 years ago

BTW, if you are using vireo for your next step, you can use -C for the folder, instead of -c for cellSNP.cells.vcf.gz, as the folder containing the sparse matrices have equivalent information.