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Input files reference and reads have incompatible contigs
I was trying to run haplotypecaller ;
- /usr/libexec/java_home -v 1.8.0_221 --exec java -jar ../gatk-220.127.116.11/gatk-package-18.104.22.168-local.jar HaplotypeCaller -R hg38.fa -I new.bams -O gatk.haplo.raw.vcf (new.bams is a list of bam files)
But getting incompatible contigs between reference and reads. I used bowtie2 and same reference fasta file for mapping, then why it is incompatible? attached is the header of one sample bam and the contigs in reference. Any help will be greatly appreciated. This error happened previously when mapping fasta was different. But why it is happening for same fasta and what is the fix? Best, Zillur