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Does Base Recalibrator require every contig to contain a known SNP or Indel?
Apologies if this seems like a duplication of previous questions but I have been unable to find an answer to my problem.
In the absence of any existing high quality SNPs upon which to base VQSR and BQSR, I have called and filtered SNPs using Haplotype Caller and am now looking to feed my HQ SNPs into BQSR. When running BaseRecalibrator, however, I receive a message saying that the contigs in my vcf file of known sites are incompatible with the contigs in my reference file. In the vcf file's header section, the contigs are the exact same length and in the exact same order as in the reference fasta file. There are 556 contigs lacking any HQ SNPs, so these contigs' names do not appear in the content of the vcf file. I assume that this is what is causing the program to fail.
I wondered if this was a bug or if it is intentional? I'm not sure how sorting the vcf, as is recommended, will help in a situation like this if not all contigs are represented in the body of the vcf?