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The contig order in knownSites and reference is not the same


I tried to use baserecalibrator. Here are my inputs:

Human reference: HG38 downloaded from GATK bundle

dbsnp_vcf: hg38.dbsnp.vcf (fileformat=VCFv4.2) downloaded from GATK bundle, sorted by Picard sortVcf
java -jar ../exe_program/picard.jar SortVcf I=hg38.dbsnp.rename.vcf O=hg38.dbsnp.sorted.vcf SEQUENCE_DICTIONARY=../ref/hg38.dict

Bam files: aligned to HG38 and sorted by Picard sortBam.
java -jar ../exe_program/picard.jar I=../test_5m/test_5m_trimmed_AG.bam O=../test_5m/test_5m_trimmed_AG_reorder.bam R=../ref/hg38.fa CREATE_INDEX=TRUE

However, I got the following error msg:
MESSAGE: Input files knownSites and reference have incompatible contigs.
Error details: The contig order in knownSites and reference is not the same
knownSites contigs = [HLA-A01:01:01:01, HLA-A01:01:01:02N, HLA-A01:01:38L, HLA-A01:02, HLA-A01:03, HLA-A01:04N...
reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15...

Can anyone give me some hint? Would deeply appreciate it.



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