Help with Base quality Score Recalibration (BQSR) using GATK

Question

[sainavyav22]

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.

Answer 1

[Shred]

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

[sainavyav22]

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