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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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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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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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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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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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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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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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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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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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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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
9
77051
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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 &...
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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 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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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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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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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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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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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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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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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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