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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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Liftover variants/vcf called on NCBI reference genome

I have been tackling this problem for a while now, and I hope someone has a better answer. I need to liftover variants (.vcf) from NCBI hg37 to NCBI hg38. The NCBI remapping tool has been depreciated. ...
Dandelion's user avatar
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Using GATK4.2 to create .idx using IndexFeatureFile for multiple vcf files

I have used GATK script : gatk IndexFeatureFile --input sampleid_hc.g.vcf to create .idx files for individual vcf files. However I am trying to create a loop and ...
user20179's user avatar
2 votes
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concatenating windowed VCF files, but quickly?

I am calling variants from WGS for a genetically diverse species which, with my sample size, produces a (bgzipped) VCF of around 500G. I am using a nextflow pipeline to chunk up the genome, call ...
nreid's user avatar
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how to annotate the effect of a genomic variant to predict what the resulting protein is?

Spoiler: This is probably a theoretical question. But, of course, if you have any tool that does this I will be extremely happy. So, I have WGS data for an organism O, both wild type (WT-O) and ...
gabt's user avatar
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How can I filter variants in a VCF file based on size?

I have a filtered VCF file with indels (no SNPs). Does anyone know of a easy way to use bcftools/vcftools to filter out small or large indels (I'm interested in indels between 50-100bp in size)? ...
bioinformaticsuser9074's user avatar
2 votes
1 answer
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How should multi allelic sites be handled in calculation per site Fst?

I'd like to calculate per site Fst(fixation index) to investigate genomic differentiation between two populations(haploid). I did SNP calling and got vcf file. In the vcf file, multi allelic sites ...
uri's user avatar
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Creating custom VCF file

I'm stuck on what seems to be a banal problem, but I can't work out where the issue is. I need to create some customised VCF files that specify particular variants of interest. This is a custom VCF I ...
Nereus's user avatar
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How to extract mutations in a particular gene from the VCF file of whole genome

Also posted on biostars I would like to extract all the mutations in a single gene of interest from the VCF file. For example I would like to extract all the mutations in the NFKB1 gene from the whole ...
Saamar's user avatar
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3 votes
2 answers
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How do I summarise VCF files?

I have got a number of VCF files that all contain data on one particular variant, with every VCF being created from an individual sample. So there is one entry per file (headers omitted): ...
Nereus's user avatar
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How to extract all variant alleles that do not match "./." from the GT column of a vcf file?

For the two vcf files linked below, I cannot find any variants in the GT column other than "./.". Is it possible to confirm if the GT column of vcf files have been annotated (i.e variants ...
CoderQ's user avatar
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How to debug a bash script

Please somebody debug my code In sub-folders there are 500000 vcf files from which I only need 500 vcf files listed in ...
Zizogolu's user avatar
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2 votes
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Is ./1 a valid GT value to add to VCF?

I have a VCF file coming from a structural variant detection tool that doesn't add GT value. I can add GT values, for example by using this tool: https://vatools.readthedocs.io/en/latest/...
risingStar's user avatar
1 vote
0 answers
54 views

tabix to subset each VCF by the coordinates given

I have a vcf file like below ...
Zizogolu's user avatar
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3 votes
1 answer
80 views

What does the absence of a variant in a VCF file mean?

I have a individual.snp.vcf.gz file of an individual genome and the referencegenome.snp.vcf.gz file of the reference genome. ...
williantafsilva's user avatar
2 votes
0 answers
90 views

Fst calculation from VCF files

I have four vcf files, SNPs_s1.vcf, SNPs_s2.vcf, SNPs_s3.vcf, and ...
hina's user avatar
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48 views

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 ...
Shafayet Rahat's user avatar
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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 ...
Alice Yan's user avatar
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1 answer
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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 ...
Dandelion's user avatar
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5 votes
2 answers
348 views

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 ...
jay.sf's user avatar
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2 votes
0 answers
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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. ...
Dandelion's user avatar
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4 votes
2 answers
119 views

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 ...
BigMistake's user avatar
1 vote
1 answer
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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 ...
Lauren Sabo's user avatar
0 votes
1 answer
62 views

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: ...
InterestingQuestions44's user avatar
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0 answers
14 views

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 ...
Akshaj Darbar's user avatar
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64 views

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 ...
Mubita's user avatar
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2 votes
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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 ...
bioinfo_comp's user avatar
1 vote
1 answer
289 views

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 ...
BigMistake's user avatar
1 vote
1 answer
144 views

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 &...
BigMistake's user avatar
1 vote
1 answer
52 views

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,...
Chris's user avatar
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277 views

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 ...
BigMistake's user avatar
0 votes
1 answer
62 views

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 ...
BigMistake's user avatar
0 votes
0 answers
289 views

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 ...
Mohamed Samir's user avatar
1 vote
0 answers
52 views

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 ...
BigMistake's user avatar
3 votes
2 answers
284 views

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 ...
BigMistake's user avatar
3 votes
3 answers
2k views

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, ...
Michael Hall's user avatar
0 votes
0 answers
77 views

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 ...
Fersal's user avatar
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1 vote
0 answers
168 views

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 ...
El K's user avatar
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2 votes
3 answers
1k views

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 ...
Pete's user avatar
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1 vote
1 answer
207 views

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 ...
Shay Maor's user avatar
3 votes
2 answers
291 views

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 ...
Macintosh's user avatar
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1 vote
1 answer
243 views

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 ...
Macintosh's user avatar
  • 160
0 votes
0 answers
97 views

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 ...
Anas Jamshed's user avatar
1 vote
1 answer
34 views

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 ...
Anubrata Das's user avatar
2 votes
1 answer
682 views

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: ...
eh329's user avatar
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3 votes
2 answers
576 views

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 ...
rseg's user avatar
  • 33
2 votes
3 answers
113 views

Interpreting short indel calls in 1000 Genomes Project VCFs

Consider the following short indel polymorphism rs59679400 on chr7. ...
Daniel Standage's user avatar
2 votes
1 answer
62 views

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 ...
agnesa rivkin's user avatar
2 votes
2 answers
56 views

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): <...
Jos's user avatar
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0 votes
1 answer
177 views

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....
Shreyas Arashanapalli's user avatar
1 vote
1 answer
961 views

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 ...
Jackson Xavier's user avatar

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