I use the gatk3.8 gatk4.0.0and gatkspark to test my data . I received a suprising result. gatk4 is slower than gatk3.8 ,and gatkspark is slower than them. The times are 17.3 vs 19.2 vs 24 min . The codes are basic and as follows:
gatk3.8
java -jar /GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar -T HaplotypeCaller -R cr.fa -I 10_dedup_reads.bam -o testgatk3.raw.variants.vcf
gatk4.0.0
/gatk-4.0.0.0/gatk HaplotypeCaller -R cr.fa -I 10_dedup_reads.bam -O 10.g.vcf.gz
gatkspark
/gatk-4.0.0.0/gatk HaplotypeCallerSpark -R cr.2bit -I 10_dedup_reads.bam -O 10.g.vcf.gz
And I am sure that the IO ,the cpus,and the memory are not reach the limit, so did I do something wrong ? Thanks a lot for reading or replying my quesion！！！