I have a .bam file generated using the hg19 release of human genome downloaded from UCSC database. Now I'm trying to indentificate genomic variants using GATK UnifiedGenotyper but it returns an error cause my bam file is Lexicographically sorted. I've tried to use Picard ReorderSam function but I've noted that my reference genome file (hg19) is in the same lexicographic order.
Is there any way to convert my hg19 fasta file in the karyotypic order? Or is there any place where I can download a version of the reference human genome sorted in this way?