Questions about using 1000 Genome bam files in HaplotypeCaller.
Dear GATK team,
I'm using GATK HaplotypeCaller in my analysis. Since there is only 10 samples in the project, I download bam files from 1000 Genome as indicated in GATK Best Practice. But the bams from 1000 Genome were aligned to NCBI37 while my bams were aligned to UCSC hg19 in GATK resource bundle. Both the contig name and length differed between those two reference. I tried reheader in samtools which didnot solve the problem. How could I handle that?