Skip to main content
4 votes

How to debug a bash script

The first two digits of vcf file names defines which sub-folder they are located. You could use this information to edit temp.txt so it contains the full path: ...
DavyCats's user avatar
  • 497
4 votes

Renaming samples in vcf file

This proved to be so simple that it took a while to discover: Just use colnames. ...
dnebdal's user avatar
  • 41
3 votes
Accepted

Creating custom VCF file

That sounds like your header isn't tab separated. You can check for the presence of tabs with od -c. So, to check the header, do ...
terdon's user avatar
  • 10.1k
3 votes
Accepted

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

The absence of a variant means the variant was not found. However, that does not mean you can assume the position in the sequenced individual was homozygous for what is in the reference. Perhaps the ...
terdon's user avatar
  • 10.1k
3 votes

Where to download a file with major and minor alleles at every position?

Sounds like you're looking for the dbSNp files. You haven't specified a species, but you can download the data for human from the dbSNP FTP site. Specifically, you want: ...
terdon's user avatar
  • 10.1k
2 votes

I am trying to create a subset of 10k variants from 25-30 unmapped contigs of a g.vcf file including the header

After some guidance from my advisor, this command allowed me to get the output file I needed. ...
Lauren Sabo's user avatar
2 votes

Converting VCF format to text for use with PLINK and understanding column mapping

However, the column names won't match exactly. I know that I can use BETA instead of OR, and FRQ might correspond to MAF, but I can't seem to find the imputation information score INFO. Yes. There is ...
BigMistake's user avatar
2 votes

Converting VCF format to text for use with PLINK and understanding column mapping

For the first part of question 2: if there are other recommended sources like dbGaP. Please refer to this Databases of GWAS summary statistics: Database Content GWAS Catalog GWAS summary statistics ...
ii4 unsafe's user avatar
2 votes

Where to download a file with major and minor alleles at every position?

I agree with @terdon that perhaps dbSNP is what you may want to look at. The dbSNP155 RefSNP VCF file in GRCh37 version may help. It can be downloaded from https://ftp.ncbi.nlm.nih.gov/snp/...
Lloyd_LiuSiyi's user avatar
2 votes
Accepted

How do I summarise VCF files?

The first step is to merge your VCFs. For this, you need to compress them with bgzip and then index with tabix: ...
terdon's user avatar
  • 10.1k
2 votes
Accepted

How to extract all variant alleles that do not match "./." from the GT column of a vcf file?

I checked one of your files, LUD.TH179.PASS.dbsnp_cosmic.vcf.gz, and can confirm that none of the samples listed in the VCF have a genotype for any of the variants. ...
terdon's user avatar
  • 10.1k
1 vote

Liftover variants/vcf called on NCBI reference genome

Could you use the hg19 --> hg38 chain from here? As I understand it, the main difference between GrCH37 and hg19 are the format the chromosomes are written (whether there is a "chr" ...
Sarah's user avatar
  • 496
1 vote

Liftover variants/vcf called on NCBI reference genome

Liftover is hard. While many variants can be lifted over relatively easily, some cannot. First, some variants are not even variants in the other genome (the other genome has the variant allele as the ...
terdon's user avatar
  • 10.1k
1 vote

How can I filter variants in a VCF file based on size?

Vcftools allows you to filter to include or not include a list of sites. https://vcftools.github.io/man_latest.html#SITE%20FILTERING%20OPTIONS If you can first grab the locations of indels of this ...
Sarah's user avatar
  • 496
1 vote

How to extract mutations in a particular gene from the VCF file of whole genome

As mentioned, there are many options to go (eg. vcftools and bcftools). The Broad Institute provides a valuable toolset (GATK) for this very purpose and extended procedures for various variant ...
44Pasha's user avatar
  • 11
1 vote

How to extract mutations in a particular gene from the VCF file of whole genome

Find the location of the gene of interest and then filter the vcf for that location using vcftools, bcftools, plink, or some other software. There is a lot of good documentation available online for ...
Sarah's user avatar
  • 496
1 vote
Accepted

Is ./1 a valid GT value to add to VCF?

No, ./1 isn't valid. You can find the VCF specifications at https://samtools.github.io/hts-specs/. The current version is VCFv4.4 and this is the genotype section ...
terdon's user avatar
  • 10.1k
1 vote
Accepted

VEP annotation INFO field Ensembl IDs and locations

You need to set your expectations clearly instead of just saying "Does not agree". I'm taking a guess here - your statement is that the 2/4 of the gene co-ordinates do not overlap the ...
Ram RS's user avatar
  • 2,310
1 vote

Invalid tag name: "1KG" and Invalid character '/' in 'SA' FORMAT field at chr1:6197766

Given issues I've had in various programming languages that use numbers at the start of a variable, the tag issue might be related to it starting with a numeric value. Is it possible to change that ...
gringer's user avatar
  • 14.1k
1 vote

How do I add reference/alternate alleles to my vcf file?

Let me know if you see any potential issues with this solution. It just replaces the dots with random letters (easier/faster than aligning to reference genome). ...
BigMistake's user avatar
1 vote

How do I calculate inbreeding on a single VCF file?

Possible solution: ...
BigMistake's user avatar
1 vote
Accepted

Check mutation of a gene

Assuming this is a diploid genome, this looks like it could be a heterozygous variant (i.e. A is present on one chromosome, and G is present on the other chromosome).
gringer's user avatar
  • 14.1k
1 vote
Accepted

Is a human genome file with reference as NCBI37 the same as hg19?

Most likely yes, they are the same. However, "NCBI37" is an odd/unusual notation, because it doesn't indicate the species (human / mouse). Assuming it's a human genome (based on you ...
gringer's user avatar
  • 14.1k
1 vote

Where do I get a large reference VCF?

For anyone who arrives here looking for a large reference VCF but not wanting GRCh37, you might consider the HGDP+1KG subset of the Genome Aggregation Database's dataset. You can find a VCF file per ...
Daniel King's user avatar
1 vote
Accepted

Where do I get a large reference VCF?

Solution: Use https://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/b37.vcf/, then to get the ancestry information (i.e., the ancestry group of each sample, e.g., "HG00566"...
BigMistake's user avatar
1 vote

How to generate rsid values locally from VCF file

Generally, consumer WGS companies do not deliver annotated VCF's. Annotations include rsIDs, gene names or similar area designations, and others. But this can be done using the NIH dbSNP VCF files ...
SurplusGadgets's user avatar

Only top scored, non community-wiki answers of a minimum length are eligible