Using the below command in GATK 18.104.22.168, I am getting:
A USER ERROR has occurred: Input files reference and features have incompatible contigs: No overlapping contigs found.
gatk BaseRecalibrator \ -I NA12878_mark_duplicates.bam \ -R /home/cmccabe/Desktop/fastq/resources/ucsc.hg19.fasta \ --known-sites /home/cmccabe/Desktop/fastq/resources/dbsnp_138.b37.vcf \ --known-sites /home/cmccabe/Desktop/fastq/resources/Mills_and_1000G_gold_standard.indels.hg19.vcf \ -O /home/cmccabe/Desktop/fastq/NA12878_recal_data.table
I am using the resource bundle from the ftp as well as the fasta. Is there a way to ignore these errors or am I doing something wrong? I also aligned with the same fasta using
bwa-mem. Thank you :).