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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17 views

Combine all alternate alleles

I have a vcf with multi-allelic SNPs, e.g. REF: A and ALT: G, C. I would like to combine all reference alleles to the most ...
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Genotype quality in VCF for haploid calls

I cannot find in the VCF specs what is the default value of Genotype Quality GQ for haploid calls. In such case, is the default the missing value ...
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42 views

Meaning of order of alleles in VCF GT field for unphased genotypes

Order of alleles in genotype field (on VCFs) can be used to infer haplotypes However, what about unphased genotypes? I have a VCF file where I only have unphased genotypes: ...
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29 views

Dictionary and index of vcf for base recalibration step

I need suggestions in creating index and dictionary with vcf files. For the base recalibration step, I downloaded Homo_sapiens_assembly38.known_indels.vcf.gz from the given link: https://console.cloud....
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If I have data from a full genome sequence, how can I search for a known pathogenic variant of a known gene?

(I apologize in advance if this question is incomplete or does not make complete sense as this is not my area of expertise. I have a CS background but am a bioinformatics neophyte.) I did a full ...
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Association test to get p values and OR in plink2, and file input format

Are there any commands for association testing in plink2 which will output p-value and OR in the resulting output file? If so, what kind of file input do I need to use for such commands...a vcf.gz ...
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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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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: ...
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164 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 ...
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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 ...
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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. ...
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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: ...
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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 ...
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122 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: ...
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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 ?
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1answer
105 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: ...
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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 ...
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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'...
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216 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 ...
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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? ...
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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 ...
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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 ...
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250 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 ...
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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 ...
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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 ...
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69 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 ...
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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 ...
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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 ...
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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 ...
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83 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 ...
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48 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 ...
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109 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. ~...
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134 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: ...
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822 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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135 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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259 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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519 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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435 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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775 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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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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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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140 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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Running a script in python [closed]

I am trying to run a script in python but I getting this error ...
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261 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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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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396 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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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 ...