The Stack Overflow podcast is back! Listen to an interview with our new CEO.

Questions tagged [vcftools]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
1
vote
0answers
25 views

vcf tools Error: Require Genotypes in VCF file in order to output Fst statistics

I want to calculate Fst by vcf tools and GATK. I did this steps: for creating gvcf: gatk HaplotypeCaller -R ref.scf.fasta -I input.bam -ERC GVCF -O out.g.vcf ...
2
votes
2answers
64 views

extracting last few lines of a growing bgzip compressed .vcf.gz file

I am running bcftools merge to create a single .vcf.gz file out of a collection of chromosomal ...
-1
votes
1answer
108 views

Parsing .vcf file for this information

I have a .vcf file https://www.dropbox.com/s/8v73nppwg3a1tnd/LP2000109-DNA_A01_vs_LP2000103-DNA_A01.SVannotated.txt?dl=0 with this header ...
2
votes
2answers
128 views

Variant calling without matched normal sample

I have WGS .bam files for 3 patients (tumour and its matched derived model namely organoid) but I don't matched normal sample. If I call variants of each patients (tumour and its matched organoid), ...
4
votes
1answer
109 views

Are duplicate variants against the VCF standard?

I have been trying to understand an error that the EBI's vcf_validator gives when run on my vcf file. Consider this minimal file: ...
3
votes
1answer
97 views

Output from vcftools missingness

I'm new to data filtering on vcf data and vcftools. I performed variant calling on my dataset, CHR22, homo sapiens. I'd like to remove sites that are missing in more than 5% of individuals. ...
4
votes
2answers
341 views

Sort vcf by contig and position within contig

Due to tabix constraints, I need to sort a vcf so that contigs and then positions within contigs occur in numerical order in the vcf. I don't know if the following will sort positions within contigs, ...
4
votes
1answer
102 views

vcftools: indel size histogram command returns empty file

I would like to get some summary statistics on a vcf file from one individual, which has over a million variant calls. I've tried to make a histogram of indel sizes with this command, ...
2
votes
0answers
82 views

bcftools consensus not working when using -H flag

Sorry, I have been trying to work this out desparately all day. Biostars couldn't find any answer so I am cross posting here. I am trying to get both the left and right reference genome using a ...
6
votes
2answers
5k views

Converting VCF file to PLINK bed/bim/fam files

I am trying to find the best way to convert VCF files to PLINK binary bed/bim/fam files, but it seems like there are many varied ways to do this. (For example, using Plink 1.9 --vcf tag, bcftools, ...
3
votes
2answers
3k views

How to subset a VCF by chromosome and keep the header?

I would like to subset a VCF which only has chromosome 2. The problem with using various grep commands, e.g. ...
2
votes
3answers
3k views

How to concatenate “by chromosome”-VCFs?

I have a several VCFs which are VCF which only contain information by chromosome. That is, there's a chromosome 1 VCF (with only chr1), a chromosome 2 VCF (with only chr2), etc. I checked to make ...