Question: removing germline polymorphism for mouse sequencing data
1
0
Entering edit mode
6.2 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 • 1.5k views
ADD COMMENT •
1
Entering edit mode
6.2 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
ADD COMMENT •
0
Entering edit mode

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 REPLY •
0
Entering edit mode

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

ADD REPLY •
0
Entering edit mode

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 REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 1403 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6