I have a general question about GATK related to the importance of known VCFs (for BQSR and HC) and resources file (for VQSR). I am working on rice for which the only known sites are the dbSNP VCF files which are built on a genomic version older than the reference genomic fasta file which I am using as basis.
How does it affect the quality/accuracy of variants? How important is to have the exact same build of the genome as the one on which the known VCF is based? Is it better to leave out the known sites for some of the steps than to use the version which is built on a different version of the genome for the same species? In other words, which steps (BQSR, HC, VQSR etc) can be performed without the known sites/resource file?
If the answers to the above questions are too detailed, can you please point me to any document, if available, which might address this issue?