So i downloaded a .bam from phase 3 1000 genomes and i want to run the RealignerTargetCreator on it using GATK 3.8.
The following command works fine:
sudo java -jar algorithms/gatk/gatk3.8.jar -T RealignerTargetCreator -R references/hg38.fasta -I data/HG100.reordered.bam -o data/HG100.realignertargetcreator.intervals
But when this command is run with -know i get contigs mismatch error between my bam and the vcf file. The know indel VCF used is located here:
Step prior I have applied the picard ReorderSam using hg38.
Am i using the incorrect indels file?
Thanks in advance.