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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How does Allele Number get determined in VCF files?
I am looking at the publicly available gnomAD v3 VCF file.
The header describes the AN field as: "Total number of alleles in samples."
This suggests to me that it should be a constant ...
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How to print alternative allele from VCF with htslib c++
I would like to print the alternative allele from a vcf file which i load in with htslib.
The description of some functions:
https://github.com/samtools/htslib/blob/develop/htslib/vcf.h
I have used ...
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2answers
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How can I subset WGS data to the level of WES variants?
I would like to compare mutational signatures1 in patients from different studies, however some studies are based on exome seq (i.e. ~20,000 coding variants) and some are from whole genome seq (i.e. ~...
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How do I obtain a vcf read from a pyvcf.Reader?
I wondered how would I be able to obtain variant based on chrom and location range.
Optimally, this function would be like:
...
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2answers
115 views
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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2answers
49 views
Produce .vcf file of ALL mutations in .bam file
I got tasked with a problem, that i thought would be quite simple to solve, but turned out to be quite tricky. Our lab is running targeted mutagenesis experiments in yeast using crispr base editors. ...
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1answer
50 views
Convert VCF to genotype table
How can I convert a VCF file into a genotype table (SNP matrix)?
I have this format:
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1answer
73 views
Download or create VCF from Human Genome Diversity Project (HGDP)
I can't seem to find HGDP data in VCF format.
Does anyone know where I can download it from?
Perhaps there a Snakemake pipeline for calling VCFs from this data?
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VCF spec: is it possible to have other alleles in addition to the MISSING value ('.') in ALTS?
I'm writing a VCF parser, so I have to consider and handle all corner cases regardless of how contrived they may seem. The specification is a bit unclear about the MISSING value ('.') in the ALTS ...
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57 views
Filtering a VCF without samples/individuals
Certain VCF files (gnomAD, dbSNP) don't have sample columns defined for individuals.
For example in this gnomAD VCF there is no sample column:
...
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1answer
164 views
VCF-merge fails due to tabix not producing .tbi files
I'm trying to use vcf-merge to combine 2 exome capture vcf files (~250K and ~330K in size) before trying it on all 96 samples. I'd appreciate any advice on the best way to do that! I've detailed what ...
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1answer
240 views
What does the number mean in an HGVSp annotation?
Let's take the example p.Arg452Pro that I got from an annotated VCF file that contains an HGVSp column.
What does ...
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37 views
Understanding snpSift/snpEff output
I am trying to check the concordance between two VCF files. Each file contains the same samples, with one being a sequencing experiment, and the other having been genotyped by SNP array.
I used snpEff/...
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Pindel has an extremely large output
I am wondering if I am doing something wrong here.
I ran Pindel (alongside two other structural variant [SV] callers) on four WGS samples. The two other callers ...
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139 views
Create a genotype matrix from VCF file using bcftools
I have a vcf file that contains SNPs from chromosome 2 for 2000 samples. I want to create a genotype matrix from this vcf file.
The file is in zipped format as well so that I can use ...
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1answer
91 views
Allele count is zero
I ran freebayes on bacterial data and got a vcf file. Some of the SNPs found have AC=0, but in the bam file I can see that there are alternative alleles, so in my ...
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1answer
56 views
Running a script in python [closed]
I am trying to run a script in python but I getting this error
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How to find the region with frequent mutation?
I am very new to bioinformatics and I was wondering if I can get some help regarding finding region that has high mutation rate.
Currently, I have 2 fasta files, one that is aligned and one regular ...
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2answers
95 views
Generate VCF from different .bam files with different chromosome names
I have two resources of .bam files. One is generated by our lab (1 sample = 1 bam). One is downloaded online (again 1 sample = 1 bam). For the downloaded samples the chromosomes are labelled: chr1, ...
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Removing common variants in the 1000 genomes database from .vcf [closed]
I have 15 .vcf files. I need to remove `common variants in the 1000 genomes database' appearing in at least 0.5% of the population
Do you know from where I may start?
Thank you so much
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2answers
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Are there any tools for discovering tandem repeats around a variant in a VCF file?
I know for example PolyX from Pierre's Jvarkit to find the number of repeated REF bases (homopolymers) around a position in a ...
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1answer
189 views
vcf file to gene annotations and or genes
Is there some tool that will convert a vcf/bcf file to some gene annotation, based on the fact that I have the gene annotation of the already exsisting reference genome. Or some tool that will give me ...
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1answer
48 views
Can someone recommend software for reference-based genotype-estimation?
Problem: I have low-coverage sequencing data from humans in vcf format. For each sample, I have PL scores / preliminary genotype calls from the software ATLAS (it's a bit like GATK for those who don't ...
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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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1answer
76 views
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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1answer
57 views
Help with the definitions of fields in a VCF output by Strelka
In Strelka vcf in INFO column we have these
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1answer
73 views
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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2answers
108 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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2answers
112 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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1answer
71 views
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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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3answers
122 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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4answers
274 views
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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2answers
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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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1answer
581 views
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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1answer
57 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
223 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
119 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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1answer
85 views
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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12 views
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
164 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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3answers
1k 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
78 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
122 views
Remove variants that do not map to human genome
[This question was also asked on Biostars]
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 ...
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3answers
447 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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263 views
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
...
