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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VCF or BAM file for raw data of gene test?

My friend has a VUS (Polymicrogyria with or without VEDS) mutation that was found in her whole-exome sequencing with respect to the phenotype given that time. At present, her doctors have more ...
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Error occurrence after merging files with bcftools: wrong number of fields?

This question was also asked on Biostars I have multiple vcf of CASES and CONTROLS variations annotated by VEP, SNPEff and SnpSift. First pair vcf -> only variations| CASES and CONTROLS Second ...
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Why does GATK produce both 0/1 and 1/0 genotypes in the same file? Are the two not equivalent?

I have always thought that 1/0 and 0/1 in VCF genotype fields are equivalent. And yet, GATK uses both. For example, these are ...
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Is it valid VCF not to 'squash' positions with more than one ALT allele?

I'm seeing output from PBWT that looks like this: ...
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Problems when using vcf2maf

I am trying to use a commonly recommended package named vcf2mafto convert vcf file to maf file and is reliant on Ensembl's Variant Effect Predictor (VEP) here. However, if I follow the guidelines ...
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Confusing result from Sanger Imputation Service (Eagle v2.4 for phasing, PBWT v3.1 for imputation)

I ran my 23andMe data through the Sanger Imputation Service that uses Eagle v2.4 for phasing, PBWT v3.1 for imputation. However, some aspects of the results are very confusing to me. Perhaps see #3 (...
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Range of values for VAF in heterozygous genotype

(VAF = variant allele frequency) This question follows from this one. What is the expected range of values for VAF of mutations with heterozygous genotype (i.e., 0/1 or 0|1)? Is it possible to have 0% ...
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Assess ploidy estimation through SNV and CNV results

I want to assess ploidy estimation (i.e., diploid vs tetraploid) in a set of samples for which I have both results from the variant caller (i.e., SNVs) and from the copy number caller. What are the ...
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How to convert a BAM file into a VCF file

I know that there is a lot of methods to do so, but most of them need to have a reference file. (For example, the GATK force me to provide a reference.) However, I think the BAM file I am working with ...
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Error in installing vcf2maf

I tried to install vcf2maf following this tutorial from GitHub: https://github.com/mskcc/vcf2maf. I get a repeat error when I try to test out vcf2maf using the code:...
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When can we have duplicated variants in a VCF file, excluding artifacts?

I read these two questions on duplicated VCF variants: 1, 2. However, it is not entirely clear to me when duplicated variants can arise (excluding merging artifacts). I want to understand if ...
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Imputing 23andMe 3v data to v4 and v5?

The 23andMe version 3 data (v3) is now quite 'old' and new data is being collected on the updated v5 Illumina SNP-Chip (details here). Is there an online service for imputing 23andMe v3 files to v4 ...
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What are values of FILTER column of vcf files produced by Mutect2

I have called SNVs with Mutect2, now in filter column of a file called filtered vcf I have a lot of things like ...
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Filtering a vcf with a text file of SNP rsIDs

I have a vcf file containing an ID field with a snps and a list of human SNPs from dbSNP.I want to remove whatever in dbSNP from vcf file. The text file is like this: ...
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Extracting a column from a vcf file

I have a zipped vcf file of dbSNP hg38 version No space left on my device to unzip that I want to extract a column from that I have tried this ...
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Topmed File Requirements

I am trying to run my VCF's through Topmed Imputation (https://imputation.biodatacatalyst.nhlbi.nih.gov/#!pages/home) I am trying to make sure that I have the correct requirements for my file to be ...
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How to process multiple VCF files present in a 2 folders and create afd plots

This question has also been asked on Biostars I have 2 directories that contains multiple VCF files. I want to write code in python that will process all vcf files and create an AFD (allele frequency ...
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imputed dosage values for vcf files

I have one more question related to genotype file. I submitted the job in michigan imputation server. and my imputed dosage for chr 22 file is: 22 16050435 22:16050435:T:C T C . PASS AF=0.00098;MAF=0....
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An error with annovar

I want to install annovar but in one particular part I always get this error ...
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VCF file inspector app with GUI

Does anyone know a good, free-to-use VCF file inspector app (Mac OS, with GUI) where I can browse the content of a VCF file similarly to bamseek*? I would like to browse SNP annotation split by ...
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Interpreting imputation result from GLIMPSE

I'm following this tutorial of GLIMPSE for learning. I was expecting some extra SNPS coming from the 1000 genome reference in the resulting .vcf file. Though I understand the phasing in the output ...
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Tutorials on phasing and imputing low-coverage sequencing data

I am new to low-pass whole genome sequencing and have the basic idea of phasing and imputation. I have .vcf file after calling haplotypecaller tools from GATK. After searching the phasing and ...
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Plink assigns all samples as control, when there are cases listed in .fam

My case and control samples are combined in one .bed. I changed my .fam file to include the phenotype value for the samples in the .bim, but they might be in a different order than listed in the vcf ...
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How to replace values in .fam file corresponding to the case and control samples (IID) of my data set?

I have a .fam file, but because the vcf used to create the .fam has no phenotypical information, and the phenotypic value column had all -9, the .fam file does not distinguish which samples are case (...
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Assigning case and control label to different samples of large merged file to input into a plink 1.9.0 association test

I have a large vcf file with both case and control samples in the file. I am planning to input the vcf into the --assoc function of plink with the --fam parameter that contains a .fam file that ...
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2 votes
1 answer
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Visualization of mutations in (part of) viral genome - existing tools?

I'm trying to visualize mutations in SARS-CoV-2 sequences, somewhat like it's done on outbreak.info: but for individual sequences, probably on the base of the vcf files generated by the ARTIC ...
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Converting Control and Case vcf files into a format that can be processed by plink 1.9.0

I have two vcf files, one containing samples with TP53 mutations, and one containing samples with no TP53 mutations. The vcf without the mutations is the control and the vcf with the mutations is the ...
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How to extract homologous sequence data from multiple .vcf.gz files?

I have short read data from multiple samples stored as scaffolds.vcf.gz files. I have some gene sequence of interest. I want to find the closest homologous sequence ...
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Ensembl Variant Effect Predictor (VEP) issue during execution

I got this error during execution, pls guide me. ...
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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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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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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 have a CS background, but am a bioinformatics neophyte I did a full genome sequence which provided me with ~100GB of files (SNP VCF, Indel VCF, BAM, Indel TBI, SNP TBI, BAM BAI, CNV VCF, CNV TBI, CV ...
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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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8 votes
4 answers
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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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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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Consensus sequence from vcf file

I am generating a consensus sequence for SARS-Cov-2. I am visually inspecting every candidate SNP in a pileup. Sometimes I find that there are two consistent variants for the same position, but I can ...
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1 vote
3 answers
242 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 ...
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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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1 vote
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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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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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1 answer
383 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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1 vote
2 answers
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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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