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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Q: What analyses can I perform with a completely phased genome assembly?
Phasing a genome is the process of determining which variants lie on which copy of each chromosome. For example, position 5,430,500 might have an A on the paternal chromosome, but a T base on the ...
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VCF's unknown ('.') values causing problems for GATK's Liftover Vcf
I am having a tough time calling LiftoverVcf in GATK. I have concatenated all of the Vcfs of interest and removed rows with problematic values but now when I run LiftoverVCF I get the following error:
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Bcftools call always assigns a genotype even if there are no reads?
I am variantcalling my 96 multi sampled bam file with samtools/bcftools however I obtain some strange results.
When I use the following command:
...
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bedtool intersect to compare .vcf file to reference genome
I have a .vcf file generated using samtools. I want to know mutations in specific genes by comparing ...
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94 views
Looping over several files in bash
I have a bash script:
I am wondering how I can change this script to loop over a bunch of .vcf files and give output .txt with the name of corresponding .vcf
I tried changes done in similar script ...
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105 views
Changing this code in a way to work for my files
I have a bash script which extracts some information from a .vcf file but one .vcf file at each time. How I can change this script in a way to work on a bunch of .vcf files and the output is a .txt ...
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Remove repeated ALT allele from the REF field of a vcf-like file
I have 200 .txt files on a Linux system. In each file, I have the reference allele in the REF column and INDELs in the ...
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105 views
awk working with large files
I have two very large vcf files 2GB and 6GB I want to look for unique combinations of CHROM and POS and output the row that matches. However, because the files a so large my machine always hang and ...
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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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Empty values in FILTER field after running Mutect2
I was expecting something like in this image:
But when I ran Mutect2, the FILTER field was empty in the output VCF file. How can I enable PASS filters?
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1answer
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Subset a multisample VCF file
I need some help with GATK. I have a multisample vcf file containing 18125 samples. After performing PCA I have around 303 samples as outliers and I wanted to remove these samples from my multisample ...
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517 views
Error while calling bcftools mpileup - Failed to open -: unknown file type
I have sequenced a bacterial genome with a GridIon from ONT. Basically what I want to check is whether or not trimming 50 bps at the beginning of the reads will improve alignment against the reference ...
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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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38 views
swap genotypes for specific fields of a vcf file
Is there a tool already established to "swap" the ref/alt information in the GT, AD and PL ...
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2answers
130 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 ...
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1answer
56 views
creating population AF from set of individuals in 1000 genomes population?
What's the recommended way to create population-level Allele Frequency variant entries from a set of individuals (vcfs?) in the 1000 genomes (or similar) project?
For example, given the IBS ...
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what is the most complete vcf file of population allele frequencies that can be built/downloaded from public datasets?
What is the most complete vcf file of population allele frequencies that can be built/downloaded from public datasets nowadays?
About 5 years or so ago, it used to be the latest release of the CSHL ...
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1answer
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SnpEff gene annotation with @ such as PCDHB@
I'm using snpEff to annotate some VCFs and getting some spurious annotations that don't have transcript ids. Some of these annotations have a gene name followed by ampersand such as PCDHB@ and I'm not ...
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1answer
88 views
Quality GL entries in vcf file
I have a vcf v4.2 file with structural variants, the 8 columns describing the variant are clear, but in the genotype information I got confused by values of ...
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555 views
Find overlap between VCF files
I have two VCF files and I want to compare the missing rate in each of them, but I want to only look at sites that are present in both files. How could I go about getting a list of positions that are ...
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1answer
77 views
Why does IGV turn a VCF QUAL of “.” into -10?
IGV is turning QUAL "." into -10 from this VCF of structural variations. I'm wondering if this means anything or if I should report a bug to the IGV devs.
Here's a row from a VCF:
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1answer
89 views
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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248 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 of variants with Plink
I have a set of SNPs (single nucleotide polymorphisms) { S1, S2, ..., SN } from approximately 200 humans. I wish to determine the linkage disequilibrium (LD) for a defined subset of these SNPs. By ...
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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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1answer
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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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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
97 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
624 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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1answer
132 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
222 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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216 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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638 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
83 views
Bash script error at paste command
I wrote script for pasting rsids on CADD output. Here is script.
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3answers
153 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
220 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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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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1answer
73 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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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
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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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1answer
80 views
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
331 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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646 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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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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91 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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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 (...
