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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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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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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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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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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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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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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What is the correct way of setting the genotype after splitting multi-allelic sites in a VCF file?
This question was also asked on Biostars
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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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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Empty values in FILTER field after running Mutect2
I was expecting something like in this image:
But when I ran Mutect2, the FILTER field was empty in the output VCF file. How can I enable PASS filters?
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structural variants: why doesn't AS + AP = SU?
I have run smoove then duphold on 46 individuals, then pasted the duphold output back into a squared vcf with all 46 samples.
I have been using SU/AC as one of my filters, looking for variants that ...
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R package grur: missing_visualization() fails during redundancy analysis of .vcf
I am trying to use the R package grur to process GBS SNP data, which is installed from github as instructed. For starters, I am running the test code in this vignette. As suggested I am running it ...
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bcftools consensus not working when using -H flag
Sorry, I have been trying to work this out desparately all day. Biostars couldn't find any answer so I am cross posting here.
I am trying to get both the left and right reference genome using a ...
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Post ipyrad filtering of SNP loci from GBS, based on SNP quality
I want to use SNPs produced by Ipyrad, which is a python script for RADseq, using maize genome data via RAxML to examine the monophyly of a highly-variable focal species and its phylogenetic ...
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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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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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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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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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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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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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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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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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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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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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Normalize by counting CNV within a pool of VCF files
I’m (trying) using the GATK4 germline CNV calling pipeline. I successfully got 57 VCFs from my sample batch, called with segments (obtained by merging the contiguous intervals), like in a classic VCF :...
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Error filtering SNPs with Plink
Im trying to filter SNPs using PLINK with this command. Also, the .map and .ped files were converted to a plink format from a vcf file (...
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Complete Genomics Junction file for SV Detection
At present, I have vcf file for each patient generated from tumor data. I am using virtual normal correction method for somatic mutation detection because I don't have normal data. For SNP or small ...
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Is a human genome file with reference as NCBI37 the same as hg19?
In other words, are NCBI37 and hg19 synonymous? I can't find much information for what NCBI37 is in a human (not mouse) genome.
Relevant line from VCF:
"##reference=NCBI37"
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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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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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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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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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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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An error with annovar
I want to install annovar but in one particular part I always get this error
...
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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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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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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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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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