Why I can not reproduce my result on different hostcomputer?
I have encounter a strange issues with GATK-3.3/3.7:
I used HaplotypeCaller to call variants on the same realn.recal.bam file, and it gave me different results when i ran on different computers (calls or annotation were not exactly identical) . I finally found that only if i ran on the same computer, i can get identical results between different repeats.
This dose not make sense, I think even if i use down-sampling, i should able to reproduce the result in any condition.I have stuck in the problem for a few days, can you give some advices? how could this happened and how to reproduce my result on different computers?
here is my commmands:
java -Xmx5G -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R hg19.fasta -I sample.realign.recal.bam -L chr1 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -dt NONE -o sample.chr1.g.vcf.gz
java -Xmx2G -jar GenomeAnalysisTK.jar -T GenotypeGVCFs -R hg19.fasta --variant sample.chr1.g.vcf.gz -o sample.chr1.vcf.gz -stand_call_conf 30 -stand_emit_conf 10 -dt NONE
PS: I kept using same java version for all my tests.