Convert VCF to pg_snp and gd_snp

, ,
1

Hi,
When using “VCF to pg_snp” (with idea to reformat later to gd_snp), Galaxy fails. The tool does not accept that some alleles have alternatives:

An error occurred with this dataset:
format interval database ?
bad variant nt AAGA,AATG for nt 2 at /cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/vcf2

Please advise on how to proceed, or on alternative tools. Thank you!

2

I am currently having the same problem. Did you find any solution for this problem?

3

I resorted to NOT using Galaxy for this.
Instead, I manipulated my vcf in vcfR and poppr, both implemented in R.

1 Like
4

Oh! Bummer! Thank you anyways!

5

All of the Genome Diversity tools have been deprecated, and are no longer supported.