[GATK 126.96.36.199] Funcotator issues.
Hi, I have questions in using Funcotator in GATK 188.8.131.52. My input vcf uses b37 (GRCh37) as a reference.
1) What are chr1_a_bed and chr1_b_bed in the resource bundle, funcotator_dataSources.v1.6.20190124s.tar.gz?
2) Would you guide me how to localize gnomAD resources? It is configured to use google cloud, which is not allowed in my computing environment unfortunately.
3) A lot of fields in Funcotator output are empty. I feel I am missing something. For over 13000 variants, I don't get any variant annotated by Cosmic, SwissProt, GO, TCGAscape, DrugBank, CCLE, CGC, ClinVar, Familial Cancer Genes, HGNC, etc. Would you help me annotate variants as much as possible?