how can i build the preprocess vcf for mouse, like human common SNP vcf file, using GATK google warehouse snp data

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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how can i build the preprocess vcf for mouse, like human common SNP vcf file, using GATK google warehouse snp data #72

Open honghh2018 opened 1 year ago

honghh2018 commented 1 year ago

Hi development, I want to demultiplex the mouse single cells data, but the SNP file can not be obtain. so i want to build it myself from the GATK mouse SNP file. Based on this reason, what can i do for this issue? how to build the mouse common SNP vcf file ?

Any advice would be appreciated. Best hanhuihong

hxj5 commented 1 year ago

Hi, you may follow the steps listed in the file scripts/SNPlist_1Kgenome.sh