In one of our projects we are comparing hg19-related assemblies (such as b37 etc) to hg38, and basically discovered that there are no available VCF files for the newest reference. I understand that it requires a tremendous effort and that's why most of the large consortia are reluctant to switch. However it seems like it would have to happen sooner or later. So, maybe some of the newest projects did in fact process everything in hg38?
Please let me know if you know of any such cases. Thank you in advance.
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predeus
There are VCFs in:
ftp://ftp.ensembl.org/pub/release-83/variation/vcf/homo_sapiens/
including 1000G. Not processed directly based on GRCh38, but instead a careful liftover from GRCh37
HTH
Thank you for the link. However, I was not interested in the liftover VCF files - since "careful" is pretty meaningless here. It doesn't really matter how careful you are if the file is not generated from BAMs aligned to a true hg38 reference.
Thank you for the suggestion anyway.
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Hello predeus!
It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?t=67585
This is typically not recommended as it runs the risk of annoying people in both communities.
I thought that ought to integrate the two and make the answers easier to find, no? :)