I have uploaded to galaxy a vcd file based on hg38 and want to convert it to hg19. I have uploaded hg38 → hg19 chain file from UCSC ftp site. When I use the galaxy tool crossMap VCF, I select VCF file, I select hg19 for 'Lift over to (FASTA file), select the chain file for ‘Source for leftover data (chain file)’. When I run it I get an error in both output datasets generated. The error message states:
tool error An error occurred with this dataset: ‘filter’ object is not subscriptable.
I don’t understand what I’m doing wrong or what the error message means. Interestingly, when I went to crossmap website , it did not state that it needed a fasta file for vcf conversion so I don’t understand why the galaxy tool has it.
Any help would be appreciated.