1000Genomes vcf file and correct reference genome used in FastaAlternateReferenceMaker giving error
I am using a vcf file from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/
Specifically, chromosome 20.
1000Genomes says their reference genome is GRCh37, which is the same as hg19. However, when I attempt to use
java -jar GenomeAnalysisTK.jar \ -T FastaAlternateReferenceMaker \ -R chr20.fa \ -o phase3_human_chr20.fa \ -V ALL.chr20.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf
I get this error:
ERROR MESSAGE: Input files /san/data/GATK/ALL.chr20.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf and reference have incompatible contigs. Please see https://www.broadinstitute.org/gatk/guide/article?id=63for more information. Error details: No overlapping contigs found
I've read through https://software.broadinstitute.org/gatk/guide/article?id=63 and have tried to fix the error myself. However, the reference genome for the vcf file was hg19, and I cannot see any other genome I can use. Could there possibly be another error I am not seeing?