I am working with three genomes from the same species. I have managed to call variants between the reference and two of the genomes but the third seems to be having an issue that I don't know. I processed them exactly in the same pipeline prior to calling the variants on them using HaplotypeCaller. However, on the third genome the algorithm produces an empty vcf file as if it encountered an exact replica of the reference genome. It doesn't seem like its encountering any type of error as the log file shows that it is walking through the genome fine and the standard error file is empty (no error messages)
My code for calling the variants is as follows:
java -Xmx6g -jar Documents/GenomeAnalysisTK-2.6-5-gba531bd/GenomeAnalysisTK.jar -T HaplotypeCaller -nct 4 -R equcab2.fa -I Documents/PhD_work/recal.bam -stand_call_conf 20 -stand_emit_conf 10.0 -o output.raw.snps.indels.vcf 1>> gatk_HaplotypeCaller.log 2>> gatk_HaplotypeCaller.stderr
I would really appreciate if someone can help me out with this.
Thank you! :-)