Tag: popmax

Hi, I use a loop for that. Something like this to inspire you: # Enter folder where gnomAD data are here: gnomAD=”/path/to/gnomAD/database/release/3.1.2/gnomad.genomes.v3.1.2.sites.” # Enter the folder where your results are and will be annotated further cd /path/to/your/results/folder/ # Enter the name of the final results’ file from SnpSift ann=”results.ann.gnomAD.genomes.v3.1.2.vcf” #…

Trim gnomAD v3.1.2 1 Hello! I’m wondering if anyone has written code, or knows of BCFTools/VCFTools/other published tool, to trim gnomAD v3.1.2 down from its current monstrosity (~3Tb for the all chromosomes) into a smaller utility for purposes of variant filtering in rare disease variant annotation. Essentially I want to…

drop duplicate insertion deletions in VCF at same position while keeping one 0 I am normalizing some GWAS summary statistics to gnomad. gnomad has some entries like this that seem to be duplicated indels: chr21 13405435 rs140129927 G GT . PASS AC=2962;AN=148224;AF=0.0199833;popmax=afr;faf95_popmax=0.0636127;AC_non_v2_XX=1118;AN_non_v2_XX=59420> chr21 13405435 rs140129927 GT G . PASS AC=40946;AN=148190;AF=0.276307;popmax=amr;faf95_popmax=0.419202;AC_non_v2_XX=16812;AN_non_v2_XX=59400…

subpopulations available in MafH5.gnomAD.v3.1.1.GRCh38 1 @b14a6f0d Last seen 16 hours ago United States Are subpopulation MAFs available for gnomADv.3.1.1 with any package, like they are in MafDb.gnomAD.r2.1.hs37d5? I’m trying to use Genomic Scores to obtain all variants in a genomic range with MAF in any subpopulation >= cutoff. I tried…

gnomAD v3 link not working for download 1 your URL is wrong. $ wget -q -O – “https://storage.googleapis.com/gcp-public-data–gnomad/release/3.1.1/vcf/genomes/gnomad.genomes.v3.1.1.sites.chr1.vcf.bgz” | gunzip -c | head ##fileformat=VCFv4.2 ##hailversion=0.2.64-1ef70187dc78 ##FILTER=<ID=AC0,Description=”Allele count is zero after filtering out low-confidence genotypes (GQ < 20; DP < 10; and AB < 0.2 for het calls)”> ##FILTER=<ID=AS_VQSR,Description=”Failed VQSR filtering…

How to calculate popmax values for gnomAD variants? 0 I’m trying to use the gnomAD data to build a noise filter. We want to filter variants from our .vcf’s that have a popmax value greater than a certain threshold, but I’m having trouble figuring out how to calculate popmax. We’ve…