Help with Base quality Score Recalibration (BQSR) using GATK
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9 weeks ago

Hi, I am performing base quality score recalibration using GATK for my whole genome sequenced data of dog. I used the following command:

gatk BaseRecalibrator \
  -R canFam3.1.fa \
  -I Tumor_canfam3.1_alignment_sorted_rmdup.bam \
  --known-sites Filtred_Published.vcf \
  -O GdT_recalibration_report.table

gatk ApplyBQSR 
     -R canFam3.1.fa \
     -I Tumor_canfam3.1_alignment_sorted_rmdup.bam \
     --bqsr-recal-file GdT_recalibration_report.table \
      -O GideonTumor_bqsr.bam

I took the known sites file from iDog snpdatabase.

I am receiving the following error message:

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

Someone please help me with this.

GATK BQSR • 277 views
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Entering edit mode
9 weeks ago
Shred ★ 1.5k

Chromosome names from VCF and input files are not the same.

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Hi, Thanks for your reply. Are you aware of vcf file compatible to canfam 3.1 reference genome?

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