Subset vcf file by column ID in other file

Hi all!

I have a vcf file from exome seq (11GB). I have another file (.txt) with only one column. I want to subset the vcf with the ID that both files have in common.

snp vcf

• 831 views • link

updated 5.7 years ago by zx8754

• written 5.7 years ago by bio.pelayo •

What have you tried? Read the bcftools manual, there is a command for your exact situation in there.

• 0 views • link

written 5.7 years ago by Ram

0 answers

No answers yet.

More posts like this

GnomAD subset vcf files
written 4.2 years ago by kanika.151

Hello All, Do you know how to extract variants related to a specific population from the GnomAD exome vcf file? In ExAC, one can find …
How to transform a whole-genome callset into whole-exome callset?
written 4.9 years ago by Alejandro Rojo •

Hi all, I have a callset from whole-genome data and with this callset, I want to transform it into exome callset by extracting the variants …
unannotated_multisample-VCF + annotated-TSV = multisample_annotated-VCF
written 5.7 years ago by bio.pelayo •

Hi all! I'm dealing with vcf and tsv files always in the same scenario: unannotated_multisample-VCF and a related tsv with annotation(from VEP). I wonder in …
Fst calculation with VCFtools
written 8.1 years ago by Dracaena •

Hi all! I am working with 2 pools of full genome sequencing data. I currently have a VCF file for each pool and one VCF …
Select a subset of variants from a larger vcf file
written 8.3 years ago by paraskevopou •

Hi all!! I have a large vcf file and I want to create a subset one according to #CHROM field with a txt file (a …
Intersection of 3 multi-sampled vcf files
written 8.8 years ago by michelle.zl.kee •

Hi, I have 3 vcf files from different samples and would like to get a file with an intersection of common SNPs found in all …
How edit VCF file (specifically #CHROM and ID columns)
written 8.8 years ago by angelaparody •

Hi, I have a .vcf file and I need to edit #CHROM and ID columns because these are problematic when I try to obtain other …
Intermediate range calculation from files
written 9.9 years ago by User 6777 •

Hi all, I have started to learn perl and python but now I am completely stuck in this problem, thus I seek your help. I …
VCF - compare
written 10.3 years ago by manojkumarbioinfo

Hi, I have 5 set of vcf files aligned using BWA and variants are called using GATK. I'm interested to find for common SNPs that …
How to compare 2 VCF files
written 12.2 years ago by Parimala Devi

Hey, I have 2 vcf files. I want to compare the two, and save the SNPs that are common to both in a separate file, …