Question: Best approach to filter variants in a noncoding region?
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gravatar for dunya1001
11 months ago by
dunya10010
dunya10010 wrote:

I have a large set of data of nearly 200 individuals who were sequenced by NGS after a GWAS was performed to identify top variants. I have fine-mapped this region (including filtering steps) using GATK, samtools, bwa etc. and currently working with VCF files of nearly 6000 variants. I have removed all multi-allelic variants manually and used VCFtools to filter for minor allele frequencies. I currently need to prioritize these variants in order to perform subsequent genotyping using TaqMan because there are currently way too many. I would also like to mention that all the individuals that were sequenced had the phenotype of interest; therefore, no comparisons can be made. Do you have any suggestions for filtering out these variants (all of which are in a noncoding region) for regulatory influence or any other parameter?

Thank you.

ADD COMMENTlink modified 10 months ago by Biostar ♦♦ 20 • written 11 months ago by dunya10010

Maybe start with FunSeq2. Includes modules to prioritize variants e.g. by calculating scores based on transcription factor motif disruption.

ADD REPLYlink modified 11 months ago • written 11 months ago by ATpoint28k

get bed file and intersect vcf with bedtools.@ dunya1001

ADD REPLYlink modified 10 months ago • written 10 months ago by cpad011212k
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