Questions tagged [vcf]

VCF, acronym for Variant Calling Format, is a text file type used to store information regarding genetic variants.

Filter by
Sorted by
Tagged with
8
votes
4answers
895 views

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 ...
2
votes
0answers
91 views

What is the correct way of setting the genotype after splitting multi-allelic sites in a VCF file?

Consider this minimal VCF file which contains a multi-allelic call made by a somatic variant caller on a human tumor sample: ...
1
vote
2answers
72 views

Renaming samples in vcf file

I am currently asking myself how to rename samples in a vcf file. This is necessary, because the naming of several samples included in thr vcf file was unfortunately not be chosen by me. I am loading ...
1
vote
3answers
58 views

Masking sites in a vcf file

I need to mask all sites in a vcf file flagged by the 1000 Genomes Project as being unfit for population genetic analyses. The sites for all chromosomes are available at: 1000Genomes masked sites From ...
0
votes
2answers
63 views

Remove repetitive region vcf file using repeatmasker bed file [duplicate]

I have a 1000 genomes vcf file for chromosome 14. And I want to remove variants in repetitive regions flagged by repeatMasker. I have a bed file for those repeats. I downloaded that file from UCSC. ...
4
votes
1answer
89 views

Annotating a .vcf with centimorgan information

Some programs (e.g. shapeit4) automatically annotate an INFO tag into a .vcf file which gives the cumulative genetic distance in cM between each SNP: ...
0
votes
0answers
47 views

How to make CIRCOS plot of VCF file?

I have 3 VCF files, I want to make CIRCOS plot just like the following: https://www.nature.com/articles/s41598-020-70527-8/figures/4 I try to follow the tutorial but could not understand. The genome ...
0
votes
1answer
87 views

Find common SNPs in multiple VCF files

I have 3 VCF files. A1.vcf A2.vcf A3.vcf I want to get the common SNPs that are present in all these three files. And output must be in vcf format. output: ...
-1
votes
2answers
65 views

Filter rows of VCF file for Match=EXACT?

How do I remove rows in a VCF file on 1kGenome column, where Match=EXACT using bash ?
0
votes
1answer
75 views

GATK 4.2 using IndexFeatureFile with multiple files

I am trying to use GATK IndexFeatureFile to create ".vcf.gz.tbi" file. But I have 480 files. For the pilot study I used: ...
0
votes
0answers
76 views

Spanning deletion conversion

I have a vcf file created with GATK with spanning deletion https://gatk.broadinstitute.org/hc/en-us/articles/360035531912-Spanning-or-overlapping-deletions-allele- and I now need to compare this VCF ...
0
votes
0answers
71 views

Convert DNA raw data between a different formats [duplicate]

I have .vcf file with partly decoded genome provided by some service. How can I convert this file into other popular formats which may be used in other services? I'...
0
votes
1answer
128 views

Making PLINK compatible files from VCF file without phenotype information

I have a big VCF file that I need to convert to, preferably, bed/bim/fam files that are readable by plink. Currently using plink 2. I am aware that this version of plink can be used to convert VCFs ...
1
vote
2answers
80 views

Obtaining Whole Genetic Sequence

As an end-user of my own data, specifically raw DNA sequence (WGS, whole genome sequencing). How or where do one obtain such DNA data so that a biology hobbyist can perform bioinformatics on this? ...
2
votes
1answer
41 views

How can I use my Myheritage DNA results file for further analysis?

I had my DNA tested by Myheritage and they sent me a csv file with RSID, Chromosome, position and result (which base) with about 700,000 rows. I understand most analyses of DNA use VCF files but is ...
0
votes
0answers
39 views

FMT/DP of missing genotypes in bcftools

I have a VCF file where the FMT/DP of missing genotypes has been recorded itself as missing data (".") When I filter ...
0
votes
0answers
162 views

Filtering samples by FORMAT attributes using bcftools

The -e and -i options of the bcftools filter command appear, by default, to only allow for ...
1
vote
2answers
51 views

Finding SNP/Indel Markers of Interspecific Variation

This is a revised version of my original question, edited to include the portions already answered by @Maximilian Press. Goal: Find SNP and indel alleles which are fixed between but lack polymorphism ...
2
votes
0answers
146 views

Allele Count and Allele Frequency in VCF files

I'm working in bioinformatics, but my computational skills far outstrip my knowledge of biology or genomics. So forgive the noobish question. According to the VCF specification, the ...
2
votes
1answer
66 views

What tools can I use to look up my alleles, genotypes, or phenotypes from my sequenced DNA (WGS)?

(I am not a Bioinformatics expert, please forgive and educate me if I've used any wrong terms or assumptions here) I bought a "Whole Genome Sequence" kit, which gave me the following VCF ...
7
votes
1answer
131 views

How to import large .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 ...
0
votes
1answer
61 views

How do I create a VCF file of all known pathogenic mutations in a gene of interest?

I would like to create a list (probably .vcf format would be good) of all known pathogenic missense mutations in a human gene of interest and then add other variants that could lead to the same ...
0
votes
1answer
28 views

Consensus on how to select SNPs for creating a phylogeny when the full dataset is too large

I have got a quite large VCF file (about 20k samples with 160k SNPs after filtering for quality etc.) and I would like to get a phylogeny for it. However, the whole dataset's too large for my ...
1
vote
0answers
78 views

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 ...
1
vote
1answer
45 views

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 ...
2
votes
2answers
92 views

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. ~...
0
votes
1answer
100 views

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: ...
2
votes
2answers
576 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 ...
2
votes
2answers
109 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. ...
1
vote
1answer
209 views

Convert VCF to genotype table

How can I convert a VCF file into a genotype table (SNP matrix)? I have this format: ...
0
votes
1answer
404 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?
0
votes
0answers
24 views

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 ...
0
votes
1answer
369 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 ...
3
votes
1answer
651 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 ...
2
votes
0answers
40 views

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 ...
1
vote
0answers
320 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 ...
2
votes
1answer
129 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 ...
-2
votes
1answer
76 views

Running a script in python [closed]

I am trying to run a script in python but I getting this error ...
0
votes
2answers
227 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, ...
-3
votes
2answers
108 views

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
1
vote
2answers
46 views

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 ...
0
votes
1answer
360 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 ...
2
votes
1answer
51 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 ...
0
votes
2answers
51 views

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 ...
1
vote
1answer
101 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: ...
1
vote
1answer
79 views

Help with the definitions of fields in a VCF output by Strelka

In Strelka vcf in INFO column we have these ...
0
votes
1answer
108 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 ...
0
votes
2answers
121 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 ...
0
votes
2answers
117 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 ...
-1
votes
1answer
76 views

Modifying .vcf files

I have 200 .vcf files like this on a Linux system: ...