Open cgpu opened 5 years ago
But look at this:
https://www.cureffi.org/2012/09/19/exome-sequencing-pipeline-using-gatk/
hg19 is the same as GRCh37, though as GRCh37 getting assembly patches from the GRC while the main chromosomes may not change some of the alternative haplotypes might not always be identical
See here: https://github.com/mskcc/vcf2maf/issues/95
Currently if using hg19 ref fasta, it complains for the VEP cache vs fasta discrepancy
For GRCh37 -> hg19, check this option from VEP cache:
--synonyms [file]
Also check here from GATK, GRCh37 vs hg19: https://software.broadinstitute.org/gatk/documentation/article?id=23390