comparing 2 VCF files

I am trying to compare two VCF file (results of small variant calling from WES data) to get overlapping and non-overlapping regions separately. what is the best tool for this comparison?

snp

• 2,355 views • link

written 5.9 years ago by Sara

See: Using BCFtools to intersect multiple VCF files

• 0 views • link

written 5.9 years ago by GenoMax

0 answers

No answers yet.

More posts like this

Calling variants/SNP for single-cell RNA-seq data
written 2.1 years ago by QX •

Hi all, I am trying to use GATK mutect2/haplotype (default option) for variant calling on a bam file from single-cell RNAseq data; however, the generated …
allele matching between identical genotypes
written 2.5 years ago by rj.rezwan •

Hi, I have the variant calling output in the form of `vcf` files. Variant calling was done with `GATK haplotypecaller`. I am interested in performing …
GIAB Benchmarking
written 2.6 years ago by Mat •

Hi, I am trying to benchmark a few variant calling softwares to compare precision and recall. I have decided to use exome data as file …
VCF evaluation using RTG.jar vcfeval
written 6.1 years ago by Sara

Hi there, I am trying to do benchmarking for my pipeline (to analyze `WES` and `WGS` `germline` and generate VCF file for `SNV and INDELs`). …
difference between DRAGEN and GATK
written 6.1 years ago by Sara

I have `WES` data and tried to make `VCF` file using `GATK4` and `DRAGEN` but got different results. for both tools I used default setting …
tool for the new protocol of WES for CNV detection
written 6.4 years ago by Sara

to identify `CNVs` using `WES` data, I am trying to use WES data from a new protocol of `Agilent Whole Exon V7 + CNV backbone` …
SNPs/InDels of VCF compared to de novo genome assembly of Mice
written 7.0 years ago by lhb032 •

Hi, I am confused about variants (mainly SNPs and InDels) detected from variant calling and de novo genome assembly. Of course, using which type of …
Comparing VCFs constructed from mapping to different reference genomes
written 7.6 years ago by kat •

Hi, I am comparing variant calling pipelines from two authors who have used different versions of a reference genome. Is there a tool that could …
peaks overlap: ATAC & CHIP seq
written 9.7 years ago by sophialovechan •

Hi guys. I have two peak files. One is from ATAC seq and the other is from H3K27ac chip seq. I am trying to merge …
Sensitivity of variant calling
written 11.1 years ago by anon •

Hi All, can someone recommend for me a tool besides GATK - GenotypeConcordance module, which can calculate the variant calling sensitivity from the comparison of …