CNV and DUP in vcf files Gnomad database · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

CNV and DUP in vcf files Gnomad database

I just wanted to confirm that the ALT in the vcf file does not contain any Structural variants CNV, DUP. I just checked (https://gnomad-public-us-east-1.s3.amazonaws.com/release/3.1.2/vcf/genomes/gnomad.genomes.v3.1.2.hgdp_tgp.chr21.vcf.bgz) for Chr21 header for ##ALT=<CNV .(https://samtools.github.io/hts-specs/VCFv4.3.pdf) It does not have them . So does that mean it must not be there for all other chromosomes? If not, how do we confirm it?

dup cnv gnomad vcf

• 643 views • link

written 4.2 years ago by arya.sagittarius •

0 answers

No answers yet.

Log in to answer this question.

More posts like this

How to liftover ALT field of the structural variant in VCFs?
written 3.7 years ago by kojix2

I have tried CrossMap.py and gatk LiftoverVcf, but neither of them seem to be able to convert the ALT field of the structural variant (SVTYPE=BND). …
What does the position column in the VCF file from PostprocessGermlineCNVCalls refer to?
written 4.5 years ago by Frieda •

Hello, PostprocessGermlineCNVCalls post-processes the output of GermlineCNVCaller and generates VCFs with deletions and duplications. According to samtools documentation (https://samtools.github.io/hts-specs/VCFv4.3.pdf), if any of the ALT alleles …
Including tbi file along with VCF when running VEP on remote dataset (GnomadV3)
written 4.7 years ago by maria2019

Hi, I am trying to run VEP on remote data from GnomadV3. I was hoping to run it remotely, without the need to download the …
gnomAD v3 link not working for download
written 4.9 years ago by peter •

I am trying to download whole genome GnomAD vcf file but every time I do it gives me ERROR 404: Not found. This is how …
Gnomad genome vs Gnomad exom (extremely rare Ref case)
written 5.9 years ago by Eugene A

Hi, I've accidently noticed that an SNP with close to 1 allele frequency in Gnomad exom does not show up in gnomad Genome and that …
Missing SNP in gnomAD hg38 liftover vcfs
written 6.9 years ago by Nicolas Rosewick

Hi, On gnomAD website there are both hg19 and hg38 vcf. hg38 vcfs are liftover from hg19. https://gnomad.broadinstitute.org/downloads I was analyzing some data using both …
What are valid VCF symbolic alternate alleles for structural variants?
written 7.1 years ago by Garrett Stevens •

I've noticed custom symbolic alternate alleles for structural variants in a few VCFs. For example, the [gnomAD SV VCF][1] ... ##ALT=<ID=CTX,Description="Reciprocal chromosomal translocation"> ... 12 …
Multiple rsIDs at chromosomal location?
written 7.2 years ago by rrbutleriii

In the [VCF format][1], there is the option for the ID field to have multiple semi-colon separated values. In theory, there could be two dbSNP …
Valid or invalid vcf? REF nucleotide is not matching reference in vcf lines where ALT equals <CNV>
written 8.7 years ago by dschika

Hi, I got a vcf file and the first I checked was if the first nucleotide given at REF matches the nucleotide in the reference …
In VCF files, what character encodings are used / legal?
written 11.2 years ago by Andrew Thomas •

In VCF files, what character encodings are used in practice? What character encodings are *expected *for the format? The examples I've seen seem to include …