How to fix "Contig chrKI270728.1 not present in the sequence dictionary " error

Question

[Yoosef]

Hello

In the first step of BQSR I get the following error. How should I fix it? At the end of message, I have written my code to perform this task.

A USER ERROR has occurred: Contig chrKI270728.1 not present in the sequence dictionary [chr1, chr10, chr11, chr11_KI270721v1_random, chr12, chr13, chr14, chr14_GL000009v2_random, chr14_GL000225v1_random, chr14_KI270722v1_random, chr14_GL000194v1_random, chr14_KI270723v1_random, chr14_KI270724v1_random, chr14_KI270725v1_random, chr14_KI270726v1_random, chr15, chr15_KI270727v1_random, chr16, chr16_KI270728v1_random, chr17, chr17_GL000205v2_random, chr17_KI270729v1_random, chr17_KI270730v1_random, chr18, chr19, chr1_KI270706v1_random, chr1_KI270707v1_random, chr1_KI270708v1_random, chr1_KI270709v1_random, chr1_KI270710v1_random, chr1_KI270711v1_random, chr1_KI270712v1_random, chr1_KI270713v1_random, chr1_KI270714v1_random, chr2, chr20, chr21, chr22, chr22_KI270731v1_random, chr22_KI270732v1_random, chr22_KI270733v1_random, chr22_KI270734v1_random, chr22_KI270735v1_random, chr22_KI270736v1_random, chr22_KI270737v1_random, chr22_KI270738v1_random,......

My code for BQSR first step:

java \
  -jar gatk-package-4.3.0.0-local.jar BaseRecalibrator \
  -I '/media/yousef/C0B0499AB04997B4/Alignmentresult/Hg38_practice/patient38_sorted_MD.bam' \
  -O '/media/yousef/C0B0499AB04997B4/Alignmentresult/Hg38_practice/BQSR1.txt' \
  -R '/media/yousef/EEFC0BDBFC0B9CC9/Sequencing/Next_generation_sequencing/Index_files/hg38_FASTA/hg38.fa' \
  --known-sites '/media/yousef/EEFC0BDBFC0B9CC9/Sequencing/Next_generation_sequencing/Index_files/VQSR_data/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf'

[Ram]

Check your ref fasta and BAM header - the error clearly states that there's a mismatch between them. You need to use the reference you used to get the BAM file in this step (and downstream steps that need a reference) as well.

[Yoosef]

I have used genome version 38 during alignment in hisat2, and its fasta format (hg38.fa) in BQSR. How should I open my .bam file? there is no software to open it on my system.

[Ram]

Install and use samtools. samtools view -H file.bam will show you the BAM header.