7
votes
Extract lines from a file based on a range of coordinates listed on a second file
If you have a VCF file with an intact header, you can use bcftools for this. All you need to do first is to bgzip and index your VCF:
...
- 2,714
5
votes
PL and QUAL values on VCF file?
The VCF specification provides the definition for the QUAL field.
However, QUAL values are often capped by variant callers to a given value. I have seen 100 being used and according to this ...
- 705
4
votes
Accepted
Extract lines from a file based on a range of coordinates listed on a second file
Using GNU awk for arrays of arrays:
...
- 176
4
votes
Accepted
Availability of information on genes in Gnomad VCF data
This question has gone through some iterations and commentary, so I've decided to just answer it, though it's more of a "homework" question. What you need to do is to look at the VCF file, ...
- 3,409
4
votes
Strategy for merging many VCFs
We created this over the pandemic when we needed to merge loads of VCFs which all have the same header and first few columns (ie same variants)
https://github.com/iqbal-lab-org/ivcfmerge
That page ...
- 41
3
votes
variant visualisation of VCF files for 30+ samples
Single sample PVCF files are generally not combinable in the way you describe. PVCF stands for "project" VCF. As far as I know, PVCF isn't defined anywhere but, it refers to a multi-sample ...
- 221
3
votes
How to generate rsid values locally from VCF file
Download the dbSNP VCF file (latest version) and map to your input VCF using bcftools annotate. You'll want to match reference sequence version (hg19/hg38) and use ...
- 1,744
3
votes
Interpreting short indel calls in 1000 Genomes Project VCFs
Older GATK was using the so-called variant model where overlapping variants were combined during calling. More recent GATK is using the allelic model where one non-reference allele is evaluated at a ...
- 6,295
3
votes
Accepted
Filter with bcftools
First of all, bcftools might be a bit of overkill if you want one specific variant. All you need is GNU grep (the default on Linux):
...
- 9,352
3
votes
Accepted
Compare my VCF to gnomAD variants
You can use vcfanno to annotate your vcf with the gnomad vcf file. There's an example config file for annotating with gnomad (along with other databases such as dbSNP) here.
- 94
2
votes
Accepted
How can I get latest .vcf files with annotation data?
Do you mean Somatic Sequence Variants?,
if so, Table 1 inside the following full-text link:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5707196/
And additional ...
- 176
2
votes
Accepted
Need to convert .bed to .vcf. Can the reference build (and necessary .fasta) be determined for a .bed file?
There are two different kinds of .bed files in bioinformatics; one related to storing genomic coordinate data and one which is part of the plink binary dataset, so ...
- 2,714
2
votes
Accepted
VCF: false insertions?
Microsatellites, minisatellites and other type of repetitive variation are a known feature of genomes.
I agree with previous comments in the sense that what you are observing here might as well be ...
- 705
2
votes
How to Recalculate Allele Frequency from a VCF File?
It sounds like your main confusion is how to calculate AF. I'll answer that right away, but I'll also suggest a Python library that you can use to do this and much more.
You're correct, the AF is ...
- 221
2
votes
Accepted
Interpreting short indel calls in 1000 Genomes Project VCFs
this is Marta from the NYGC. Thanks for reaching out with your questions.
The full SNV/INDEL callset that we released (listed as "SNV/INDEL VCFs" in the key resource table in our paper) ...
2
votes
How to generate rsid values locally from VCF file
As a partial answer to the specific questions about definitions:
rsIDs define a specific location and type of variation*, but the location of that variation can change within different reference ...
- 13k
2
votes
Strategy for merging many VCFs
I ended up using an iterative approach (inspired by this post), which took 1.5 hours - so a massive speed up (and that was just the sequential version).
Note: fd is ...
- 643
1
vote
Strategy for merging many VCFs
Perform a tree based merge of the files.
Sort the files into groups that can easily be merged in a measurable amount of time.
Merge each group into a separate Variant Call Format (VCF) file
Has the ...
- 111
1
vote
Accepted
Converting a Dante Lab VCF file
If your file doesn't contain the rsIDs, you can use a tool like Ensembl's VEP to annotate the file and get rsIDs as well. Of course, not all variants have an rsID so don't expect to find one for ...
- 9,352
1
vote
Accepted
Non-ACGTN alternate alleles in VCF
That isn't a valid ALT field according to the VCF standard:
ALT — alternate base(s): Comma-separated list of alternate non-reference alleles. These alleles do not have
to be called in any of the ...
- 9,352
1
vote
Accepted
what does ALT ID DUP refer to when ALT ID for copy number are already specified?
The details will depend on the specific tool used to generate the VCF. Each tool has its own system and there is not much standardization for these fields. That said, the likeliest situation here is ...
- 9,352
1
vote
Interpreting short indel calls in 1000 Genomes Project VCFs
Often multi-allelic sites would be split into several lines (one per alternate allele) to make filtering easier for specific types of alternate alleles (e.g. filter out MNV vs SNV).
VCF-level, one ...
- 705
1
vote
Maintaining SNP names when calculating allele frequencies from a VCF file on plink 1.9
The standard and most common way to name SNPs is by using rsIDs.
The reason your output from PLINK does not include SNP names is because these are not included in the original VCF you are working with....
- 705
1
vote
Accepted
Can I discard missing alleles?
If you can, do not discard missing allele information.
Generally you often benefit from being able to distinguish between a position that you interrogated and genotyped as REF (reference) versus one ...
- 705
1
vote
Accepted
convert GT:PL format to GT:GP format
Currently you have phred-scaled genotype likelihoods or PL values. Genotype likelihoods give the likelihood of observing the read data (i.e. the number of reads which map to either the ref or alt ...
- 1,442
1
vote
How can I get latest .vcf files with annotation data?
According to your answer I tried to get the files which might be useful regarding annotation:
- 206
1
vote
Compare my VCF to gnomAD variants
I haven't checked how fast this is but you could try using Hail (disclaimer: I'm a maintainer). You'll need to install the GCS connector first to read from Google Cloud Storage:
...
- 221
1
vote
Compare my VCF to gnomAD variants
If you have sufficient available disk space, you could download the files from the gnomad downloads page and use a bedtools intersect command to find the overlapping variants.
However, the recommended ...
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Only top scored, non community-wiki answers of a minimum length are eligible