Extracting specific gene sequence from VCF

Hi, how would one extract a specific gene sequence from a VCF file? I have downloaded the whole genome in VCF format and have tried doing this in IGV without success.

rna-seq

• 1,830 views • link

written 9.2 years ago by neoantu 0

what do you mean with "gene sequence" ?

• 0 views • link

written 9.2 years ago by Pierre Lindenbaum 17K

0 answers

No answers yet.

More posts like this

How to extract mutations in a particular gene from the VCF file of whole genome
written 2.7 years ago by saamar.rajput 8

I would like to extract all the mutations in a single gene of interest from the VCF file. For example I would like to extract …
Extract MAF for vcf file
written 5.6 years ago by Sumeet 2

Hi All, I have a vcf file and would like to extract MAF from dbSNP corresponding to each SNP from the vcf file. Doing it …
Extracting specific SNPs from VCF
written 7.1 years ago by igor 0

Hi, **How should I extract specific SNPs from VCF file (30x). What is the standard way of doing this? Which tool/s should I use?** I …
Detection of SNPs
written 8.5 years ago by kamel 7

Hi Biostars, I have detected SNPs in whole genomes by GATK and I have .vcf files. my question is how I can extract SNPs from …
How to get nucleotide sequence from BAM file
written 9.4 years ago by davonairos 0

Hi everyone! I apologize in advance for my ignorance. I'm just beginning in in a new bioinformatics project. I have a BAM file generated from …
VCF file that does not have genotyping data
written 9.4 years ago by beneficii 6

So, I've got a VCF file of my whole genome sequence. I've used vcftools and plink to convert it into a bed file I merge …
Extract CDS from an extracted gene without bioperl
written 9.4 years ago by adeena_hassan 5

HI everyone I have extracted genes from whole genome using bedtools getfasta command and now I want to get CDS of each gene by using …
Visualize Mutation Frequency
written 9.7 years ago by justinms 1

I currently have mutation data for a small patient cohort, for a particular gene, in VCF format. My goal is to visualize the frequency or …
how to extract the variants using Bed file
written 10.7 years ago by k.manojkumar2991 1

Hello all, Sorry if this has been answered before (though I have not found an appropriate answer already) What is an effective way to extract …
How to convert GTF format to BED format?
written 11.8 years ago by M K 66

Hi All, I am going to check mapped reads that I got from tophat, and I want to use IGV to look for specific genes …