Applying Snp Masking In Primer Creation

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10.7 years ago

sfcarroll ▴ 80

I am working with a biologist, and am building an integrated workbench feeding data from COSMIC into Primer3. It is all working well, and Primer 3 is generating assays via parameter files fed from the command line.

Using coordinates available in COSMIC -- ftp://ftp.sanger.ac.uk/pub/CGP/cosmic/data_export/Request_based_exports/UCSCMutExp_v66_250713.csv.gz -- I have extracted the mutation DNA sequence from the hg19.2bit file available from UCSC. File: http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit

Now the biologist has asked me to ensure assays do not fall on SNPs, and suggested I use a SNP-masked version of the genome. I have found several SNP directories under http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/snp138Mask/

There are also earlier versions, such as snp137. Is this the correct location to find a SNP masked copy of the reference genome?

edit Related question: Correct reference genome for COSMIC

ucsc fasta • 2.3k views

ADD COMMENT • link updated 10.7 years ago by Malachi Griffith 19k • written 10.7 years ago by sfcarroll ▴ 80

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I know I can look at the region in the UCSC genome browser, but was wondering if there was a programmatic way of doing this?

ADD REPLY • link 10.7 years ago by sfcarroll ▴ 80

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