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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

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honghh2018 opened this issue Sep 7, 2022 · 1 comment
Open

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

honghh2018 opened this issue Sep 7, 2022 · 1 comment

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@honghh2018
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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
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hxj5 commented Sep 11, 2022

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

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@honghh2018 @hxj5