I have a gVCF of ~2.5k samples from a study W. then I have a VCF of ~8k joint called samples from 3 different studies: X, Y, Z.
I want to do a joint PCA analysis of common variants in all samples from study W, X, Y, Z without joint calling. To do this I found all variants in the 3 joint called samples with gnomAD AF > 5% and whose MAF across these 3 studies is > 10%.
I pulled out those variants from the gVCFs for each sample in study W and combined it into one by file.
Next I am going to combine the VCF of studies X, Y, Z and the gVCF of study W .
One possible hitch is that the gVCFs have <non_ref> in every ALT column (either alone or with "base, <non_ref>")
What considerations are there to when merging a gVCF with a VCF?
•
written
by
jon.klonowski
1 answer
https://catherinehardwicke.com/divatrim-keto-review/ https://k12.instructure.com/eportfolios/9191/Home/StopWatt_Energy_Saver https://catherinehardwicke.com/one-shot-keto/ https://canvas.drieam.nl/eportfolios/10068/Home/StopWatt_Energy_Saver_Review https://canvas.drieam.nl/eportfolios/9780/Home/One_Shot_Keto https://www.journalism.co.uk/press-releases/blaux-bidet--cleaner-and-more-gentle-than-toilet-paper/s66/a773366/
Log in to answer this question.
-
Merging gvcf files between Dragen and other calling tools
written by tacrolimus
-
Non Variant Sites in GVCF File
written by saamhasan55 •
-
DRAGEN gVCF files and joint calling GATK-GenomicsDB
written by brunomiwa •
-
GATK joint genotyping
written by puddingmeow516 •
-
Convert gVCF to VCF with ALT allele instead of the <NON_REF> symbolic allele
written by maira.r.rodrigues •
-
Can I use Stouffer's Z method to do meta-meta-analysis or second order meta analysis?
written by andreas131298 •
-
GATK finding rare variants
written by Seigfried
-
Generation of incorrect heterozygous calls after left normalization using bcftools
written by nkausthu •
-
generate oncoprint from input VCF file
written by shu2010 •
-
post-mortem brain gene expression, comparing tissue sample points across brains
written by avari
