I tried to have funcotator annotate some germline variants. Here is my command in mac zshell terminal:
lc % gatk Funcotator --variant ./chr3q.vcf --reference ./reference/GATK/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta --ref-version hg38 --data-sources-path ./reference/GATK/funcotator/funcotator_dataSources.v1.7.20200521g --output chr3q_funcotated.maf --output-file-format MAF
However, I ran into following error:
A USER ERROR has occurred: Input files reference and features have incompatible contigs: Found contigs with the same name but different lengths: contig reference = chr1 / 248956422 contig features = chr1 / 249250621.
I download both the fasta hg38 and funcotator data source bundle from GATK. I noticed that the contig reference chr1 / 248956422 is from hg38; while the contig features = chr1 / 249250621 actually match GRCH37 chr1 length shown in the following screenshot, which is hg19. I specified in --ref-version hg38. What causes this error, and how to fix it?? I want to use hg38 because my variants are called using hg38 ref. Thanks for any help.
