Question: Question: removing germline polymorphism for mouse sequencing data
0
gravatar for Jung-ho Kong
2.8 years ago by
Jung-ho Kong0 wrote:

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.

ADD COMMENTlink modified 2.8 years ago by Kevin Blighe67k • written 2.8 years ago by Jung-ho Kong0
1
gravatar for Kevin Blighe
2.8 years ago by
Kevin Blighe67k
Republic of Ireland
Kevin Blighe67k wrote:

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

ADD COMMENTlink written 2.8 years ago by Kevin Blighe67k

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!

ADD REPLYlink written 2.8 years ago by Jung-ho Kong0

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

ADD REPLYlink written 2.8 years ago by Kevin Blighe67k

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?

ADD REPLYlink written 2.8 years ago by Jung-ho Kong0
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