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 to generate rsid values locally from VCF file
I recently used Dante to obtain a WGS and have downloaded several files produced during this process. There is a file that ends '.vcf' which I did think was a VCF file but I'm not sure now after a ...
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Converting a Dante Lab VCF file
Is there an easy way to grab the rsids (hg38) of a VCF file? I know one of the tabs can contain RSIDs, but this file doesn't contain any.
I have a software I created for mapping 23AndMe DTC testing to ...
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Non-ACGTN alternate alleles in VCF
I was trying to left normalize my vcf file using following command:
bcftools norm -f reference.fasta -m -any input.vcf > output.norm.vcf
However this gives the ...
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variant visualisation of VCF files for 30+ samples
I am relatively new to genome analysis and would like to compare 30+ vcf files, 1 sample per file. After filtering there are about ~20 variants per vcf file.
I would like to evaluate to mutational ...
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How to Split VCF File into male and Female groups
Cross-posted on biostars
I have trio_example.vcf file and I want to split them into male and female groups. I tried this:
$ bcftools query -l trio_example.vcf
And ...
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what does ALT ID DUP refer to when ALT ID for copy number are already specified?
ALT ID CN2, CN3,CN4,CN5 are regions of elevated copy number relative to the reference, Then what does the ID =DUP separately cover? I am new to these analyses. please help
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How to Recalculate Allele Frequency from a VCF File?
I have a VCF file with 200 samples (mitochondrial genome of Plasmodium falciparum). Here is a pic to take a look at:
And a few relevant lines from the actual file:
...
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Extract lines from a file based on a range of coordinates listed on a second file
I would be highly appreciated to have a script able to perform the following operation:
Only extract scaffold_1 lines from file1.vcf in which POS number (column 2) falls within column 2 and column 3 ...
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Interpreting short indel calls in 1000 Genomes Project VCFs
Consider the following short indel polymorphism rs59679400 on chr7.
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Availability of information on genes in Gnomad VCF data
I was wondering does the gnomad genome data that is downloaded in the vcf format on variants contain information on what is the nearest gene and is the genomic location available exome/intron?
if yes ...
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VCF: false insertions?
I'm working with gvcf files, containing also non-variant positions. I have noticed some insertions that I'm not able to correctly interpret or handle. An example (selected samples from a huge vcf):
<...
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Maintaining SNP names when calculating allele frequencies from a VCF file on plink 1.9
I downloaded the following vcf file from https://www.internationalgenome.org/.
http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502....
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Need to convert .bed to .vcf. Can the reference build (and necessary .fasta) be determined for a .bed file?
I have some .bed files (and .bim and .fam files) containing data for a number of different samples, and I need to convert them to .vcf.
I've found bed2vcf which is ...
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Help sought with GWAS and vcf files, lack phenotype labels
This question has also been asked on Biostars
Hi, I am very new to this area, and I am taking a class about bioinformatics. For an independent project assignment, I need to do a GWAS. I am using the ...
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Filter with bcftools
I want to filter a SNP, specifically CHROM1:POS:630128. I tried to use bcftools for this.
I came up with the following variant ...
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Can I discard missing alleles?
I am converting a biallelic VCF into a SQL table and one of my tables will be something like:
...
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Is picking variants belonging to a specific group of genomes from VCF file possible?
GnomAD has publicly available VCF files that have variant data gathered from over 15k individuals. For a university project, I want to randomly select 1k of these individuals and get the variant data ...
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PL and QUAL values on VCF file?
I want to filter my VCF file to include only the relevant information I need but I have some questions about the results I got.
This is what the first 10 lines of my VCF file looks like:
...
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BAF and LRR calculation and usage
I'm working with a vcf file, in particular I'm trying to identify a gene duplication in a sequenced genome.
I studied bcftools cnv command, but for this tool is needed a vcf file containing a BAF and ...
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Benchmarking for variant identification using RNA-seq data
I am in need to benchmark the variant identification pipeline which uses RNA seq data alone without any matched-normal. I would like to know the reference dataset (and the pipeline on which the ...
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Is it common to get different number of SNVs+Indels across samples from vcf files generated using GATK and DRAGEN (counts are higher for GATK)?
We have 2 vcf (Whole Exome Sequencing (WES) data; germline samples) files (e.g., vcf_1 and vcf_2). vcf_1 was generated (Ref. genome: hg38) using the GATK pipeline for 250 children and their parents ...
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Compare VCF files
I have two strains, X and Y, and I would like to compare the variants found in both. I have my own parent strain, Z, that was sequenced and assembled to be used as the reference genome.
I first ...
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SNPs with high population differentiation from 1k Genome dataset
I am trying to reproduce the results from this paper "Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences".
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Production database system for storing vcf records
I’m standing up a production bioinformatics pipeline that’ll be producing standard VCF files. I’d like to store this data in an SQL database that ingest the VCFs and allow me and my team to easily ...
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Converting from VCF to PLINK while maintaining the SNP names from the VCF file
Just as the title says, I am working in PLINK 1.9 trying to convert the following VCF into a PLINK file (binary or not either is fine), while maintaining the SNP names from the VCF file. I am on ...
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Polygenic Risk score calculation using vcf files
I have about 750 vcf files and I am looking to generate a Polygenic Risk Score for each individual. I am planning to use either PLINK or LDPhred to generate a Risk Score. I have phenotype information ...
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How can I get latest .vcf files with annotation data?
I'd like to perform the annotation (1000genomes, COSMIC etc.) of my variants using SnpSift and SnpEff, however so far all I get are vcf files for separate chromosomes:
http://ftp.1000genomes.ebi.ac.uk/...
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Compare my VCF to gnomAD variants
I have a VCF with small variant calls against HG38 and I would like to determine which of those calls are present in the gnomAD database.
Is there an existing tool that can do this? Should I be ...
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Are the GIAB reference genomes (HG00N) fully phased?
Specifically, the NISTv4.2.1 HG002 dataset here (more info on Genome in a Bottle). According to their README, the HG002 v4.2.1 VCF should be fully phased.
For HG001, HG002, and HG005, we have phased ...
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Weird data in VCF file
I am using GATK HaploTypeCaller for SNP calling. I have 300 samples. As far as I understand that if a sample is missing a SNP it should be denoted by ./., however, I am getting a lot of values like 0/...
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syndip dataset for benchmark variant
I have a question about syndip dataset : https://github.com/lh3/CHM-eval .
I'm struggling to find the syndip vcf.
In the release ( https://github.com/lh3/CHM-eval/releases ), we have a file named : <...
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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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