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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Fst calculation from VCF files
I have four vcf files, SNPs_s1.vcf, SNPs_s2.vcf, SNPs_s3.vcf, and ...
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Generate simulated bam for certain snps
I want to benchmark my DNA sequencing pipeline. In order to do that I want some gold-standard files in every step(.vcf,.bam,.fastq). I want to generate/simulate a bam file of reads for a given set of ...
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How do I calculate inbreeding on a single VCF file?
I would like to know the level of inbreeding for a single sample VCF file. I'm agnostic to the specific method of measuring inbreeding; any should work. However, I'd like to avoid having to specify a &...
CommunityBot
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Convert genotyping results to vcf or other plink formats
I used a Genotyping software called T1K to generate KIR genotyping, the output file contains genes and alleles for each sample, how can i convert the results to a vcf file or other formats which can ...
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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 ...
CommunityBot
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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 ...
CommunityBot
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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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VEP annotation INFO field Ensembl IDs and locations
I have a vcf file that I annoteted with VEP, for human data. I have run VEP to annotate my files with some additional parameters (as shown below in the ##VEP-command-line).
However, my output is ...
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Where to download a file with major and minor alleles at every position?
I want a list of all variants, i.e. sites which are known to vary between human to human. For example, it should ideally cover all sites in here, but without samples.
I don't want a giant reference ...
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Converting VCF format to text for use with PLINK and understanding column mapping
I successfully completed Nature PRS tutorial, which is based on PLINK. Turning to my real data, I downloaded ukb-d-20544_1.vcf.gz. Now I'm facing the problem that I seem to be unable to use it in ...
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INDELS in PLINK files converted to VCF
I want to compare/validate variants called from sequencing data with array (plink format) variant data. I converted the plink files (.bim, .bed, and .fam files) with plink1 to vcf files.
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I am trying to create a subset of 10k variants from 25-30 unmapped contigs of a g.vcf file including the header
My objective is to take a g.vcf.gz file and from 25-30 unmapped contigs with titles like "NW_020192317.1", I want to make a subset of ~10k variants from each of the unmapped contigs and make ...
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What tools can I use to look up my alleles, genotypes, or phenotypes from my sequenced DNA (WGS)?
I bought a "Whole Genome Sequence" kit, which gave me the following VCF files (this service did not include any analysis, just the raw data):
cnv.vcf
<...
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How to subset samples from a VCF file?
I have VCF files (SNPs & indels) for WGS on 100 samples, but I want to only use a specific subset of 10 of the samples. Is there a relatively easy way to pull out only the 10 samples, while still ...
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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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Invalid tag name: "1KG" and Invalid character '/' in 'SA' FORMAT field at chr1:6197766
I have a VCF file that is of the following format:
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Adding BAF and Log2 ratio to VCF file
I have access to pre-processed VCF files from a genetic dataset, and am trying to use the MoChA tool to calculate mosaic chromosomal alterations in this dataset. However, MoChA requires BAF and ...
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bcftool merge of 5K samples makes ID a large string
I am using bcftools to merge 5000+ vcf files using this command
bcftools merge -l list_of_vcfs.txt
I am getting the following error
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Correctly coding indels for ped/map files in plink and VCF
I have a challenge with how to correctly code indels in plink (I plan to convert my binary file set to VCF and use it for lift over in downstream analysis).
For instance, my dataset has an indel with ...
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How do I add reference/alternate alleles to my vcf file?
Here are the first few columns of my VCF v4.2 file. As you can see, the alt allele is missing. The VCF's refs and alts don't correspond to the reference genome.
#CHROM
POS
ID
REF
ALT
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77051
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Check mutation of a gene
Hi all, I am checking if a gene which around 50k base pairs has mutation. So is that a variant from A to G? Would you please tell me how to do so? Thank you so much!
The reference sequence from GRCh38,...
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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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How do I fix chromosome-specific Michigan Imputation Server error (Imputation on chromosome 14 failed. Imputation was stopped)
I am imputing human genome samples, all hg19, using the Michigan Imputation Server. The input of the data is one VCF per autosome, which each VCF containing a few dozen samples.
The samples within the ...
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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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Where do I get a large reference VCF?
I would like to download a large .vcf file containing many (hundreds or thousands) of samples. Ideally, I would download different population-specific .vcf files, but the ability to sort/filter by ...
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Is a human genome file with reference as NCBI37 the same as hg19?
This question was also asked on Biostars
In other words, are NCBI37 and hg19 synonymous? I can't find much information for what NCBI37 is in a human (not mouse) genome.
The VCF is from a lab ...
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What is the current state-of-the-art for classifying the ancestry groups of VCF files?
I'm wondering which tool or program is:
Most updated; doesn't use a superseded algorithm
Runs very quickly (ideally, under 30s per VCF file)
Able to be automated in some way for a large number of ...
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Extracting information from VCF file for many specific positions in specific chromosomes?
I have an excel file that I created from VCF file for common SNPs across 6 samples. This excel have the chromosomes and the position of the SNPs only (see example table1)
Now I would like to obtain ...
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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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Strategy for merging many VCFs
Can anyone suggest a strategy for speeding up VCF merging?
I have ~44,000 single-sample VCFs that I am trying to merge into a multi-sample VCF with bcftools merge, ...
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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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How to convert VCF files to input file format required by XP-CLR1.0 software?
I attempt to do a selective sweep analysis by using the software XP-CLR1.0. My genotypic data is VCF format, so I wonder if someone with experience on this package could recommend any tool to convert ...
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Title: Error merging VCF files: "The REF prefixes differ: G vs A"
I'm trying to merge two VCF files, but I'm running into an error message that says ...
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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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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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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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how to filter a multi-VCF for sex-specific genotypes?
I have a single VCF file of variants for a population that includes males & females and I would like to pull out all variants that are sex-specific. For example, sites where all males are 0/1 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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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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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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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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Interpreting short indel calls in 1000 Genomes Project VCFs
Consider the following short indel polymorphism rs59679400 on chr7.
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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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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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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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