I tried to run GATK BaseRecalibrator using the reference hg38 genome and known sites from console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0.
I used this same hg38 genome file for aligning the paired FastQ files with bwa-mem and used the known sites as following:

hg38/resources_broad_hg38_v0_1000G.phase3.integrated.sites_only.no_MATCHED_REV.hg38.vcf
hg38/resources_broad_hg38_v0_1000G_omni2.5.hg38.vcf.gz
hg38/resources_broad_hg38_v0_1000G_phase1.snps.high_confidence.hg38.vcf.gz
hg38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf
hg38/resources_broad_hg38_v0_Homo_sapiens_assembly38.known_indels.vcf.gz
hg38/resources_broad_hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
hg38/resources_broad_hg38_v0_hapmap_3.3.hg38.vcf.gz

The command was:

gatk BaseRecalibrator -I SP01c_marked_dup_sorted_RG.bam -R ../genomelib/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta --known-sites hg38/resources_broad_hg38_v0_1000G.phase3.integrated.sites_only.no_MATCHED_REV.hg38.vcf --known-sites hg38/resources_broad_hg38_v0_1000G_omni2.5.hg38.vcf.gz --known-sites hg38/resources_broad_hg38_v0_1000G_phase1.snps.high_confidence.hg38.vcf.gz --known-sites hg38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf --known-sites hg38/resources_broad_hg38_v0_Homo_sapiens_assembly38.known_indels.vcf.gz --known-sites hg38/resources_broad_hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz --known-sites hg38/resources_broad_hg38_v0_hapmap_3.3.hg38.vcf.gz -O SP01c_recal_data.table")

The error was shown as follow:

A USER ERROR has occurred: Input files reference and features have incompatible contigs: Found contigs with the same name but different lengths:
   contig reference = chr15 / 101991189
   contig features = chr15 / 90338345
   reference contigs = [chr1, chr2, chr3, ..., HLA-DRB1*16:02:01]
   features contigs = [chr1, chr2, chr3, ..., chr22, chrX, chrY]

There was no output file. For the versions, I use a Windows 10 Enterprise Build 19042 and WSL2 with Ubuntu 18.04, openjdk version 11.0.9.1, bwa version 0.7.17-r1188, and gatk version 4.1.9.0.

I'd like to know how what caused the error in this incompatibility and how to fix it since I used all resources from the official resource bundle.



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