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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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Remove variants that do not map to human genome

I received an hg38 VCF file that's had variants imputed with 1000 genomes. I've encountered some issues with the VCF; REF alleles that do not align to a reference genome, ALT alleles that do not ...
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3answers
73 views

Index VCF file for rapid access by rsID?

With tabix one can index a VCF file for rapid variant retrieval based on genomic position. I'm wondering if there are any tools that will index a VCF file to allow rapid retrieval using rsIDs and/or ...
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How to compute LD for pairs in Plink

I have a set of SNPs (single nucleotide polymorphisms), S1...SN, from approximately 200 humans. I wish to determine the linkage disequilibrium (LD) for a defined subset of these SNPs. By this I mean e....
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1answer
61 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 ...
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35 views

how do I convert a vcf file for a GWAS study (using R package vcfR)

I have a vcf file with individual level genetic data, that I read using the R package vcfR ...
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1answer
58 views

Filter VCF for “CAF=[0.9,0.1]”

Related to this other question but in this case the CAF is defined as "An ordered, comma delimited list of allele frequencies...". I tried using vcffilterjdk and the command suggested by Pierre <...
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1answer
65 views

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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2answers
187 views

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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43 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: ...
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2answers
192 views

Selecting 65000 SNPs where AF is close to 0.5 in all or most populations

I am evaluating the tool somalier (https://github.com/brentp/somalier) and I need to create a list of about 65,000 SNPs where the allele frequency (AF) is as close to 0.5 as possible across the most ...
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2answers
75 views

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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structural variants: why doesn't AS + AP = SU?

I have run smoove then duphold on 46 individuals, then pasted the duphold output back into a squared vcf with all 46 samples. I have been using SU/AC as one of my filters, looking for variants that ...
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92 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, ...
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R package grur: missing_visualization() fails during redundancy analysis of .vcf

I am trying to use the R package grur to process GBS SNP data, which is installed from github as instructed. For starters, I am running the test code in this vignette. As suggested I am running it ...
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1answer
67 views

Bash script error at paste command

I wrote script for pasting rsids on CADD output. Here is script. ...
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3answers
110 views

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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4answers
58 views

how to filter a multi-VCF for sex-specific genotypes?

I have a single VCF file of variants for a population that includes males & females and I would like to pull out all variants that are sex-specific. For example, sites where all males are 0/1 and ...
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2answers
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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). ...
3
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1answer
55 views

How to paste RSIDs in CADD output

I want to paste RSIDs in CADD output as CADD does not give RSID column in its output. For this purpose I am using bedtools intersect to compare two files and have RSID column in my CADD file. This is ...
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0answers
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How to use FastQTL with LeafCutter?

I am following along with the example data in the LeafCutter documentation and I am a bit stuck on the final step of using FastQTL to generate QTL maps. Documentation for FastQTL is scant and so are ...
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0answers
150 views

Combine VCF files

I have a problem with using rbind to combine VCF files using the library VariantAnnotation from Bioconductor. I am reading two VCF files, when I try to combine ...
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3answers
89 views

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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1answer
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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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1answer
188 views

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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2answers
340 views

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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2answers
102 views

High Phred Quality score VCF file

I am working on ION Torrent S5 XL and I am facing to an issue with VCF output generated by the variant caller of thermofisher. It stating on VCF 4.1 that Phred Quality Score is on a range of 0 to 255. ...
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1answer
65 views

How to convert files to ADAM format?

I would like to convert BAM and VCF files to ADAM format. How do I do that?
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81 views

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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Normalize by counting CNV within a pool of VCF files

I’m (trying) using the GATK4 germline CNV calling pipeline. I successfully got 57 VCFs from my sample batch, called with segments (obtained by merging the contiguous intervals), like in a classic VCF :...
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2answers
188 views

How to filter for “CAF=0.5747,0.4253”

In my gzipped VCF file I have many variants, and they report allele frequency such as: ...
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0answers
67 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 ...
3
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2answers
155 views

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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1answer
217 views

update dbSNP ID

I have used dbSNP build 138 to tag 'rs' ID in my VCF file. But later I came to know that now dbSNP build 150 has been released. I want to update the rs IDs in my VCF file. I tried but I found a ...
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1answer
37 views

How to add OVERLAP_BP field to VEP output?

I'm using the Ensembl Variant Effect Predictor (VEP) to annotate VCF files, and I am trying to add some additional fields to the output, among these is OVERLAP_BP, ...
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118 views

Error filtering SNPs with Plink

Im trying to filter SNPs using PLINK with this command. Also, the .map and .ped files were converted to a plink format from a vcf file (...
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2answers
249 views

GATK CombineVariants complains the contig order in the VCF files

I have called variants on two strains of C. elegans separately. I now want to merge the VCF files into one using the following code: Create a sequence dictionary of the reference sequence Sort the ...
4
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1answer
124 views

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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1answer
352 views

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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46 views

Complete Genomics Junction file for SV Detection

At present, I have vcf file for each patient generated from tumor data. I am using virtual normal correction method for somatic mutation detection because I don't have normal data. For SNP or small ...
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2answers
1k views

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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1answer
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How to get unique somatic mutations for each individual patients

I have exome data 32 patients. My aim is to identify unique somatic mutations in each patients. For this I have completed my pipeline for Whole Exome Data analysis using various tools like BWA mem, ...
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2answers
4k 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, ...
5
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1answer
141 views

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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0answers
63 views

Post ipyrad filtering of SNP loci from GBS, based on SNP quality

I want to use SNPs produced by ipyrad analysis of GBS data in RAxML to examine the monophyly of a highly-variable focal species and its phylogenetic relationships with about 40 congeners. An initial ...
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2answers
2k views

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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2answers
1k views

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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2answers
2k 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. ...
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3answers
2k 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 ...
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1answer
201 views

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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2answers
241 views

Approximate matches with bedtools intersect

I am using bedtools to test whether a set of variant calls produced by a new method is missing any variants from a set of known validated variants. ...