Looking for a specific heterozygous sequence variation (Lys170Stop) in a particular gene; I have a VCF file

Question

[adam]

I have a VCF file (filtered SNP) from a whole genome sequence performed by Dante Labs.

I'm looking to see if I have a particular variant of a gene, whose mutation is identified by Lys170Stop.

How can I look at both of my alleles for this particular gene to see if any contain this particular variant?

Apologies in advance if this is a silly question - I have a CS background an no experience with bioinformatics. Thanks for your help

Answer 1

[Pierre Lindenbaum]

convert the position 'Lys170Stop' to a genomic position Amino Acid Change To Genomic Location then look at your VCF if you have any variant at that position: bcftools view indexed.vcf.gz "chr12:345-345"

or just extract the portion of the gene from your vcf bcftools view indexed.vcf.gz "chr12:345-567" and annotate with VEP: https://www.ensembl.org/Tools/VEP

[adam]

Thanks so much - the web-based transvar site worked great for for Lys170Stop and I was able to locate the variant successfully using bcftools. However I'm having trouble with certain other amino acid changes, such as RDH12:Arg169Gly and TULP1:IVS14+1 using transvar, error being no results found. Is there an additional step required for these variants?

I tried using backlocate as it looks perfect for the task, but I can't figure out how to obtain the ucsc.gtf -or human_g1k_v37.fasta files. I thought I had it working, but then got an error, "A sequence dictionary is missing ... a reference should have an associated .dict and .fai file."