You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
In the recent release of 500,000 genomes, the UKB has provided SV calls, but only in bgzipped sample-level vcf files.
I've tried merging these files in groups to create a pVCF- after unzipping each vcf, as survivor doesn't seem to take .gz files? - but the file size is growing such that I can't merge those groups (I get a "Killed" error). I tried trimming the vcf files to just genotypes in the FORMAT field using bcftools - but then the merging was odd, in that when merging two files with 9000 people each in, I got only 2 individuals in the output
Do you have any suggestions for how I could perform this analysis?
Cheers,
Gareth
The text was updated successfully, but these errors were encountered:
Hi,
In the recent release of 500,000 genomes, the UKB has provided SV calls, but only in bgzipped sample-level vcf files.
I've tried merging these files in groups to create a pVCF- after unzipping each vcf, as survivor doesn't seem to take .gz files? - but the file size is growing such that I can't merge those groups (I get a "Killed" error). I tried trimming the vcf files to just genotypes in the FORMAT field using bcftools - but then the merging was odd, in that when merging two files with 9000 people each in, I got only 2 individuals in the output
Do you have any suggestions for how I could perform this analysis?
Cheers,
Gareth
The text was updated successfully, but these errors were encountered: