I am trying to run Recalibration stage from SNP calling for whole genome sequencing data. But, my reference genome do not have a known sites VCF file. So the -knownSites option is removed from my command line and i encounter the following error (Picture in Attachment):
My question is here, is it necessary for the reference genomes that do not have a known sites VCF file to perform the Recalibration step?
Cod i run:
java -jar /home/m.rafiepour222/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef/GenomeAnalysisTK.jar -R /home/m.rafiepour222/GCF_000471725.1_UMD_CASPUR_WB_2.0_genomic.fa -T BaseRecalibrator -I /home/m.rafiepour222/1_BBKHU01_F/1_BBKHU01_F.sort.rmdup.bam -o /home/m.rafiepour222/1_BBKHU01_F/1_BBKHU01_F.grp enter code here
As seen in the image, the error is associated with the same known sites VCF file...