Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
gatk3.8 vs gatk4 va gatk4spark ,the newer the slower!!
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:
java -jar /GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar -T HaplotypeCaller -R cr.fa -I 10_dedup_reads.bam -o testgatk3.raw.variants.vcf
/gatk-220.127.116.11/gatk HaplotypeCaller -R cr.fa -I 10_dedup_reads.bam -O 10.g.vcf.gz
/gatk-18.104.22.168/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！！！