dbsnp150.txt

[Teresita Díaz De Ståhl]

Dear UCSC genome service!

 

 

I wonder is there any way I can convert the variants in snp150.txt to a vcf file where the minor allele frequency is included in the vcf file and the value is calculated as in the one reported in the UCSC genome browser.

In other words I would like to annotate my sample.vcf files with the population frequency as reported by UCSC (in a stratified form and not for with the allele frequency in different populations)

Thanks a lot!

 

Kind regards

 

 

Teresita Ståhl

 

Teresita Díaz de Ståhl, PhD., Assoc. Prof.

Department of Oncology-Pathology

Cancer Center Karolinska, CCK R8:04

Karolinska Institutet

SE-171 76 Stockholm, Sweden

+46-8-517 721 35 (office)

E-mail: Teresita.Di...@ki.se

 

 

[Jairo Navarro Gonzalez]

Hello Teresita,

Thank you for using the UCSC Genome Browser and your inquiry.

The UCSC Genome Browser does not have an automated way to add frequency to a VCF file. However, the tool bcftools annotate might be of use. You would need to process snp150.txt to construct a file for bcf annotate's -a option, and use the -c option to specify the columns of the file.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro 
UCSC Genomics Institute

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