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GATK HaplotypeCaller run
I am using HaplotypeCaller for variant calling on GATK version 3.2.2 on whole genome Illumina reads. I used the following command as per best practices with and without multithreading option (-nct).
java -jar /GenomeAnalysisTK-3-2-2/GenomeAnalysisTK.jar -T HaplotypeCaller -nct 10 -I infile.re.recal.bam -R /genome/human_g1k_v37.fasta -o outfile_raw.vcf -stand_call_conf 30 -stand_emit_conf 10 -minPruning 3
Without -nct option variants found : 207828
And with -nct option variants found: 207850
Can you please help me understand why 22 extra variants found with multithreading option? And your suggestion whether to use multithreading option or not?
Thank you in advance.