Question: removing germline polymorphism for mouse sequencing data
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3.5 years ago

Thank you so much in advance. My question is how can I use data provided from dbSNP to remove germline polymorphism for mouse? I used mm9 mouse reference genome to map variants. Do dbSNP provide germline polymorphism for mm9 as well, or would I have to change my mouse reference genome to mm10? Thanks.

sequencing germline polymorphism reference • 1.0k views
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3.5 years ago

The last release for mm9 appears to have been dbSNP version 128. The file can be accessed here (direct link): http://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/snp128.txt.gz

See Here about how you can convert this to VCF / BCF, if needs be.

Kevin

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Thank you very much Kevin! Just one more thing, could you please tell me in detail how to use dbSNP to filter out polymorphisms? I'm new to this field and trying to learn. Thank you so much!

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Hello friend. In which format, curently, is your list of variants? - VCF?; PLINK format?; ... Excel spreadsheet?

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Variants are in VCF format. Would I have to convert the above data to VCF as well and would there be a tool to do so?

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