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error using bqsr and incompatible contigs

Using the below command in GATK 4.0.6.0, I am getting:

A USER ERROR has occurred: Input files reference and features have incompatible contigs: No overlapping contigs found.

Code:

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 :).

gatk bqsr
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updated by Biostar Biostar • written by bioguy24 bioguy24

Can you check the dbsnp file and ensure the contig names match those in the ucsc.hg19.fasta? I think the problem might lie there.

• 1 views • link
written by Ram Ram

The warnings is hinting you have different chromosome names somewhere. Examine the fasta, bam and vcf and check if they all use chr1, chr2, chr3, and so on; or they all use 1, 2, 3, and so on.

• 1 views • link
written by h.mon h.mon

Thank you both very much :).

• 1 views • link
written by bioguy24 bioguy24

1 answer

Upon closer inspection, I see you are mixing hg19 and b37 references. Although they are largely the same, they are not identical, and there are more differences than just chromosome naming convention:

  • differences in mtDNA sequence
  • different REF bases at some SNPs

You should use the exactly same reference for all resources (reference genome for mapping and reference vcfs).

Further discussions:

What's the difference between b37 and hg19 resources?

problems in hg19 and b37 compatibility

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written by h.mon h.mon

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