I have a large vcf file with genomic data (330 GB) and an index file that accompanies it. I ran the command:
bcftools view -f PASS...
36 results in 0.0031 seconds.
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How to regenerate an index file for a gzipped vcf file?
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vcftools and bcftools disagree
Hello,
I'm trying to impute my data using HRC (sanger server). For that I validated and annotated my vcf using GATK and then prepared... -
Spurious dosage coefficient of determination in imputed VCF file
I have a VCF file that has dosage r^2 in the info field. The problem is that while the r^2 value should be in the 0 to 1 range, it has both negative values... -
vcftools flags --mac and --max-mac give empty output
Hi everyone!
I'm a newbie in NGS data analysis, that’s why I’m asking for some help in things that might be easy in fact.
I have... -
VCFtools whole genome data zipped
Hi all!
New here, introduction: I investigate inbreeding in an endangered species where I have whole genome data of several individuals and variants... -
Filter by completeness with VCFtools
Hello,
What is the best way to filter for completeness with VCFtools?
Basically, I would like to only keep SNPs that are present... -
vcftools --minGQ not filtering
Hello,
I am trying to filter based on GQ < 15. I do the following:
vcftools --vcf infile.vcf --minGQ 15 --recode --out... -
VCFtools 012, no header?
Hi all,
Aren't we suppose to have a header on 012 files generated with VCFtools? Here is my code line:
vcftools --vcf file.vcf... -
Vcftools to convert vcf to plink, help
I have been trying to use vcftools to convert a vcf file into plink ped and map files.
If I separate my vcf by chromosome, then the it... -
Filter VCF using external Allele Frequency
Hello,
I would like to filter large multi-sample VCFs using allele frequencies obtained from VCFs or tab files from the EVS and 1000G datasets.... -
VCFtools output after comparison
I ran VCFtools to compare 2 vcf files. It ran successfully. I have output with me.
I have trouble understanding its header:
... -
Vcftools output in "012" format is empty
Hi everyone,
I've been trying to get vcftools to alter my vcf files (97 samples, around 1,000,000 variants) into matrix format, however the ".012"... -
VCFtools filtering problem
I'm having some issues filtering individuals out with a GQ below a given threshold.
Using the command ./vcftools --vcf AST.txt --minGQ... -
Filtering over 10 vcf files
Hi there, does anyone know a tool where I can compare more than 2 vcf files at once? I have 10 samples and I want to get common variants among them. I... -
what is the meaning of vcf-stats output for shared snps??
this was answered . . .
One of the output files of vcf-stats tool, (*.shared), seems to indicate it counts only only sites where the samples...
