Exome sequencing and linkage analysis : obtain a list of SNPs

Question

[wester1086]

Hello everyone, this is my first post on biostars.

I'm currently working on linkage analysis with exome data.

I'm trying to get a list of reference SNPs which are within target capture intervals.

So I have a bed file with all intervals targeted by WES (Agilent Sureselect V5 with UTRs included) , and I would like to get a list of 1000 Genomes SNPs (rs#) which are located in these intervals.

My first idea was to use biomaRt with ENSEMBL SNP database, but it doesn't seem to work as the number of SNPs located in capture regions is too large (I get an error: "Error during query execution: Got a packet bigger than 'max_allowed_packet' bytes")

Do you know any alternative method or solution to the biomaRt problem? Any help would be appreciated.

Thank you for your time.

Answer 1

[Emily]

You could try getting the VCF files directly from 1000 Genomes, then running VCF tools vcf-query on them for your regions. You could probably script this in some way.

Answer 2

[wester1086]

Thank you for your answer!

I ended up using bedtools --intersect with VCF files from 1000 Genomes and my bed file.