I have used the flowing command for GATK Relaigner target creator while running this command i am ending with the error message as shown below
Command " java -XX:-DoEscapeAnalysis -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R hg19.fasta -I bwa_mem_RG.bam -known Mills_and_1000G_gold_standard.indels.b37.vcf -o Aln.intervals"
ERROR MESSAGE: Input files /home/bioinformatics/Documents/Ocular tumor/Sample9/Mills_and_1000G_gold_standard.indels.b37.vcf and reference have incompatible contigs: No overlapping contigs found.
##### ERROR /home/bioinformatics/Documents/Ocular tumor/Sample9/Mills_and_1000G_gold_standard.indels.b37.vcf contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y]
##### ERROR reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM]
I tried to sort my reference genome sitll it shows the error.