Questions tagged [vcf]
VCF, acronym for Variant Calling Format, is a text file type used to store information regarding genetic variants.
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Is there an easy way to create a summary of a VCF file (v4.1) with structural variations?
I got a bunch of vcf files (v4.1) with structural variations of bunch of non-model organisms (i.e. there are no known variants). I found there are quite a some tools to manipulate vcf files like ...
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How to subset samples from a VCF file?
I have VCF files (SNPs & indels) for WGS on 100 samples, but I want to only use a specific subset of 10 of the samples. Is there a relatively easy way to pull out only the 10 samples, while still ...
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How do I carry out an ancestry/admixture test on a single VCF file?
This is a question from /u/beneficii9 on reddit. The original post can be found here.
Through the Personal Genome Project, I have had my whole genome sequenced by Veritas, and have it in the form of ...
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What's the difference between VCF spec versions 4.1 and 4.2?
What are the key differences between VCF versions 4.1 and 4.2?
It looks like v4.3 contains a changelog (specs available here) but earlier specifications do not.
This biostar post points out one ...
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Given a VCF of a human genome, how do I assess the quality against known SNVs?
I'm looking for tools to check the quality of a VCF I have of a human genome. I would like to check the VCF against publicly known variants across other human genomes, e.g. how many SNPs are already ...
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How to read structural variant VCF?
The IGSR has a sample for encoding structural variants in the VCF 4.0 format.
An example from the site (the first record):
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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, ...
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Converting a VCF into a FASTA given a reference with Python, R
I am interested in converting a VCF file into a FASTA file given a reference sequence with Python or R.
Samtools/BCFtools (Heng Li) provides a Perl script ...
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Tools to create annotated table of variants from VCF
The problem: I have a VCF file, a reference genome, and a bunch of annotations for the reference (genes, repeat regions, etc.) as GFF or BED files.
What I would like is a tool that takes all of this ...
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How can I extract only insertions from a VCF file?
I'm looking to subset a standard VCF file to generate one which only includes insertions (i.e. not indels).
I can get part of the way there with:
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Selecting sites from VCF which have an alt AD > 10
I have high-depth variant calling created using the HaplotypeCaller with --output_mode EMIT_ALL_SITES I'm interested in finding all sites (regardless of genotype ...
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Converting a BAM file into VCF
I have NGS illumina RNA-seq reads from M. musculus (mm10). I am trying to find variants along the strand portion of the reads in the refseq (mm10).
I mapped a pair of sequence files and generated a ...
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Tools to do VCF to MAF and MAF to VCF conversion?
Normally, I would use the vcf2maf scripts to convert a VCF to a MAF (or vice versa).
This is great software, but on my system, perl scripts with dependencies are easy to break. (Here it uses VEP.)
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calling diploid SNVs from long reads
I'd like to call diploid SNV variants from long-reads data (~80SMRTcells PacBio).
I have generated a draft reference genome for an indivudual from a heterozygous (~4%) species (Canu+Haplomerger2).
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How to import a large amount of .bed, .gff, .vcf, .paf, .sam files into an SQL database?
Are there best practices to load different bioinformatics file formats such as VCF, BED, GFF, and SAM to SQL databases? I am wondering how people out there do that efficiently.
All of these three ...
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Best practices for deciding if two structural variants are actually the same variant?
I know that I can use bcftools isec to compare two VCF files containing single nucleotide variants (SNVs); it will generate four possible output files: one with all ...
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How to manipulate a reference FASTA or bam to include variants from a VCF?
I have some software which takes fastas as the input. I need to include SNVs and InDels from a VCF into the reference hg38 and then use this.
The problem is, I don't know of an algorithmically sound ...
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How is the GT field in a VCF file defined?
As my question in SO was closed and asked to be posted in this forum, I am posting it here.
I am not from the bioinformatics domain. However, for the sake of analysis, I am trying to pick up certain ...
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How to convert the .vcf (imputed) file with GT:GP format to GT:DS?
I have the genotyped data from impute2 output in .gen format (imputed to 1000G P3). The file has genotype posterior probabilities (GP:3 values per variant). I have converted .gen to .vcf using qctools ...
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Are variant calling files personally identifiable information?
This question is to be read in the context of data protection. It seems to be common understanding that the whole genome sequence of an individual is personally identifiable, non-anonymizable ...
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GRCh38 vcf file with common cancer mutations
Is there a vcf file on the GRCh38 assembly with common cancer mutations I can download somewhere? Maybe from one of the big international cancer genomics consortia?
By common, I mean whichever ...
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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.
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How to check if indels in VCF files are left or right aligned?
I downloaded a VCF file from dbSNP, and I'm curious if the indels in the file are left-aligned for GRCH37 genome. The documentation doesn't say anything.
How can we tell if a VCF file has left or ...
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ethnicity check either from bam or vcf files
What tool could I use to check the ethnicity of a human bam or vcf file? I would like to use the results as a QC check to know whether a given sample or set of samples match the ethnicity information ...
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How to represent a deletion at position 1 in a VCF file?
I am writing a small script to write a VCF file from short multiple sequence alignments, and stumbled into an interesting corner case.
This is the way a deletion should be represented in VCF format (...
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Merge 2 VCFs from different variant callers
I am working with WES data for detection of somatic variants and I have used two variant callers because no variant caller is complete in itself. I have used GATK Haplotypecaller for small variants ...
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VCF merge containing CNV
How do I merge VCFs files containing CNVs?
I use vcf-merge, a VCFtools function, and after bgzip and tabix, SAMtools, to index and tab separate variants, but I don't know if it is the right way.
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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 ...
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Any fast options to query large VCF bed intervals?
I'm doing some analysis and I need to subset a large VCF file (~8GB gziped) given a bed interval and identify within a subset of rsid.
Unfortunately, both my normal choices to do this analysis (<...
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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, ...
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Why does GATK produce both 0/1 and 1/0 genotypes in the same file? Are the two not equivalent?
I have always thought that 1/0 and 0/1 in VCF genotype fields are equivalent. And yet, GATK uses both. For example, these are ...
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Meaning of the FORMAT fields of the VCF file coming from GIAB project
After reading the GIAB paper in https://www.biorxiv.org/content/early/2018/05/25/281006 and its Figure 1, I am still having trouble understanding the data inside the GIAB VCF file for HG001 (...
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bcftools filtering all files in a directory
Probably a silly oversight on my part, but I'm trying to filter all the vcfs in a directory with bcftools using a simple loop. My basic command is working fine:
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No variant found using GATK 4.0 HaplotypeCaller
I am doing variant calling on RNA-seq datasets from wheat which is hexaploid,the binary alignment (BAM) files were created using STAR version 2.6.0c and variant calling was done using GATK 4.0 ...
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bcftools output vs. bgzip
I've got what seems like it should be a simple question, but I can't seem to figure it out from google. bcftools has 4 output options:
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How can I remove (non-trivial) duplicates from a VCF file?
This is related to the question I asked here. Consider a vcf file that contains duplicate variants, but where the duplicates aren't simply the same thing in the same notation but instead one is a ...
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Bash script error at paste command
I wrote script for pasting rsids on CADD output. Here is script.
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Can a data file in VCF format be converted into FASTA?
I'm considering purchasing the 'MyGenome' product by Veritas Genetics to analyze my genome for a project. I'd like the data to be in FASTA format, but Veritas only provides VCF data. Is it possible to ...
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How to indicate the END of a haplotype block in VCF?
In VCF I know how to indicate that two genotypes are in the same phase by using consecutive "0|1" and "1|0" genotype fields, for example. However, how do I deal with the case that the first two ...
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Sampling haplotypes
I am trying to simulate different genome of peoples, I have data (VCF files) of various genes from the 1000K Gene project.
I want to simulate different whole genomes i.e generate a new population by ...
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Keep Format and Individual fields when annotating VCF with VEP
I'm currently updating my Variant Calling Pipeline by switching the VCF annotating software from Annovar to VEP for a variety of regions, not least how easy it is to annotate with HGVS notation and ...
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Converting VCF format to text for use with PLINK and understanding column mapping
I successfully completed Nature PRS tutorial, which is based on PLINK. Turning to my real data, I downloaded ukb-d-20544_1.vcf.gz. Now I'm facing the problem that I seem to be unable to use it in ...
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Is there a standard tool used to convert a VCF to a BEDPE?
Many popular SV callers output a VCF. Unfortunately, there isn't a unified system at the present to label events with the same notation.
However, is there a standard method for converting these VCFs ...
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Searching tool to calculate phase/switch error rate
I'm looking for a tool which, given a truth vcf file and a test vcf file, calculates the phase/switch error rate. I performed phasing of a vcf using WhatsHap and want to compare the outcome to some ...
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Simplest way to work out structural variant type?
In VCF 4.2, a structural variant (SV) can be described with the BND keyword in SVTYPE. For example, the following example is an ...
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Is it possible to check if a patient has the HLA-B27 antigen from his exome stored in a VCF file
Is it possible to check if patient has the HLAB27 antigen by comparing his exome stored in VCF with all known HLAB27 variants?
For instance, rs4349859 is a known HLAB27 SNP.
If I can find rs4349859 ...
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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,
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Fix dash/empty ALT alleles for deletions in VCF
I have a VCF file that has deletions specified like this, with the REF allele containing only the deleted portion and the ALT allele just saying -:
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Protein sequence from patient data
Currently, I am working on NGS data and my aim is to get significance prediction of variants present in the vcf file. As we know about SIFT Score for significance score prediction, I am trying to ...
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Using Python, how to convert a pandas DataFrame into a VCF?
Let's say I have a pandas dataframe with fields CHROM, POS, ALT, ...
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