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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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Multiple Samples Per Individual Query #126

Closed sxf-ux closed 5 months ago

sxf-ux commented 5 months ago

Hi I had a question.

I have 10x single cell sequencing data. I have multiple samples per individual. Ive read previous questions on similar issues here but im still a little confused.

how would I run cellsnp-lite ? I have seperate bam files and seperate barcodes for each samples. so what would the command line code be?

Also, I would want my cell barcodes to follow a structure of barcode_sample as I have that structure for other cell barcodes in other analysis. how would cellsnp-lite recognise the barcodes belonging to one samples vs another?

im running this as a prerequisite of running mquad for mitochondria variant calling so in theory, id want one vcf file that accounts for all of my samples together per individual.

thank you in advance

hxj5 commented 5 months ago

Hi, I assume you want to get the SNP results per individual instead of per sample, you may first update the CB tag in (sample) BAM files and also corresponding barcode file (to follow a structure of barcode_sample), then merge the BAM files per individual. The cmdline would be like (per individual) cellsnp-lite -s <merged BAM file> -b <merged barcode file> ...... <other options>

sxf-ux commented 5 months ago

Yes I did. Thank you for the reply. I'll try this out !

sxf-ux commented 5 months ago

it worked. thank you !