19 votes
Accepted

Converting a BAM file into VCF

It's not really possible to convert bam to vcf. bam is a mapping file, it does not contain ...
15 votes
Accepted

Is there public RESTful api for Gnomad?

As far as I know, no but the vcf.gz files are behind a http server that supports Byte-Range, so you can use tabix or any related API: ...
  • 1,473
13 votes
Accepted

The state, limitations and comparisons of large variant stores

An epic question. Unfortunately, the short answer is: no, there are no widely used solutions. For several thousand samples, BCF2, the binary representation of VCF, should work well. I don't see the ...
  • 6,023
8 votes
Accepted

Remapping genomic coordinates to account for indels

I think that you need a LiftOver Chain file to transform your coordinates. You can obtain such a file using bcftools consensus with the ...
8 votes
Accepted

How to read structural variant VCF?

I just received a reply from 1000Genomes regarding this. I'll post it in its entirety below: Looking at the example you mention, I find it difficult to come up with an interpretation of the ...
  • 19.3k
7 votes
Accepted

How to represent a deletion at position 1 in a VCF file?

From the latest VCF specs (page 8): REF - reference base(s): Each base must be one of A,C,G,T,N (case insensitive). Multiple bases are permitted. The value in the POS field refers to the position of ...
7 votes

How to manipulate a reference FASTA or bam to include variants from a VCF?

GATK has a solution that might work for you: FastaAlternateReferenceMaker, which : "Given a variant callset, this tool replaces the reference bases at variation sites with the bases supplied in the ...
  • 841
7 votes
Accepted

Given a VCF of a human genome, how do I assess the quality against known SNVs?

To achieve (at least some of) your goals, I would recommend the Variant Effect Predictor (VEP). It is a flexible tool that provides several types of annotations on an input .vcf file. I agree that ...
  • 366
7 votes
Accepted

Are duplicate variants against the VCF standard?

No. The only point the specification makes is that: It is permitted to have multiple records with the same POS I suspect this is intended to let the file list different variants occurring at the ...
  • 350
6 votes
Accepted

What is the distribution of indel sizes in a healthy human genome? of insertion:deletion ratios?

One of the 2015 papers from the 1000 genomes project has a nice figure (figure 1) showing the size distribution of medium to large sized insertions and deletions: From another 2015 1000 genomes paper,...
  • 19.3k
6 votes

Is there public RESTful api for Gnomad?

The new gnomAD site (as of August 2019) says no, no API yet: How do I query a batch of variants? Do you have an API? We currently do not have a way to submit batch queries on the browser, but ...
  • 716
6 votes
Accepted

SNP vs Point Mutation

The difference between the two depends on to whom you talk ;) You are right: both refer to one base difference from the sequence. Usually the term "mutation" is used if the change has an impact on ...
  • 1,332
5 votes

How can I find mutations associated with disease in human histone residues?

Ensembl contains this information: When you go to the “phenotype” menu item of a given gene, you will see a list of variants (potentially after clicking on “ALL associated variants”) with their ...
5 votes

What is the distribution of indel sizes in a healthy human genome? of insertion:deletion ratios?

Genome-In-A-Bottle (GIAB; version 3.3.2) contains 3.21M SNPs on auto+X chromosomes and 0.51M INDELs in 2.58Gb confident regions. The ins:del ratio is 0.92. On the CHM1-CHM13 pacbio assembly (European ...
  • 6,023
5 votes

Given a VCF of a human genome, how do I assess the quality against known SNVs?

The greatest protein coding variant catalogue is definitely ExAC (>65k individuals). They also published a blogpost where they describe how to reproduce figures in the paper (it is a good start how to ...
5 votes

remaining human genome variation that hasn't been sequenced?

In theory, almost any base in the human genome may mutate, so you have billions of variants to go. Ok, this is not so useful. A related and potentially useful question is: given a human, what is the ...
  • 6,023
5 votes

Converting a BAM file into VCF

You can use Freebayes, provided you have your BAM file and the reference genome. Example: freebayes -f genome.fa aln.bam > var.vcf I'd suggest you go through ...
  • 2,656
5 votes
Accepted

Protein sequence from patient data

Ensembl now have a tool called Haplosaurus (still in beta) which will convert your phased VCF into actual protein sequences. Haplosaurus haplo is a local ...
5 votes

Selecting 65000 SNPs where AF is close to 0.5 in all or most populations

Just use bcftools view for filtering: $ bcftools view -i 'AF>0.3 && AF<0.7' input.vcf.gz > output.vcf To truncate this list to 65,000 SNPs count ...
  • 1,332
4 votes
Accepted

How to get unique somatic mutations for each individual patients

If what you want is to split the main VCF file into 1 file per sample, you could use bcftools query and view commands. A similar question was asked on biostars, adapting Jorge Amigo's solution to ...
  • 595
4 votes
Accepted

How to manipulate a reference FASTA or bam to include variants from a VCF?

You could convert VCF to BED via vcf2bed --snvs, vcf2bed --insertions, and ...
4 votes

Merge 2 VCFs from different variant callers

The merge utility from SURVIVOR seems to be what you are looking for. I did not try it yet, but it seems to be especially designed to handle SV. The simplest thing to do would probably to first merge ...
  • 595
4 votes

How to read structural variant VCF?

So, first off, as others have pointed out, I'm pretty sure that example is just wrong. At least, the numbers don't match as you've pointed out. That said, it is impossible to be sure without showing ...
  • 8,235
4 votes

Given a VCF of a human genome, how do I assess the quality against known SNVs?

Your best bet is to use programs that provide you an complete annotation of variants present in your VCF. Two examples are snpEff and Annovar. These programs work on known variants deem different ...
  • 182
4 votes

Is there public RESTful api for Gnomad?

You can browse gnomAD variants with ClinGen Allele Registry (there is API spec available).
4 votes
Accepted

Output from vcftools missingness

Humans are diploid, so you can expect to see up to 2*N (2*68=136) alleles, so N_DATA is the number of observances of that allele.
4 votes
Accepted

How to interpret amino acid representation

This means that at position 383 the Cysteine(C) is mutated to a Serine(S). Depending on the organism and gene usually the mutation notation is linked to a specific transcript since the position could ...
  • 2,576
3 votes

How can I find mutations associated with disease in human histone residues?

I found DisGeNET useful for my purpose, a database that associates genes with diseases and, if known, gene variants with diseases. It integrates several sources of information for computing a score of ...
  • 1,022
3 votes

GATK CombineVariants complains the contig order in the VCF files

Answered in the GATK forum Try regenerating the index files for your VCFs. Picard SortVcf doesn't do it for you iirc, so when GATK looks at the index files (before opening the VCFs themselves) it ...
3 votes

How to manipulate a reference FASTA or bam to include variants from a VCF?

There's a vcf2fq sub-program that was written as part of vcfutils to convert a VCF file into a fastq file given a reference sequence. Unfortunately this doesn't ...
  • 12k

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