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.
Different coverage metrics between GATK and PICARD
I want to evaluate the panel performance by calculating the target coverage.
Both GATK and PICARD offered great convenience for the calculation. However, slightly difference was observed.
And it seems that PICARD can not calculate the percentage of target base larger than pre-defined coverage as GATK, by using -ct option. Is there any option?
java -jar /bioinfo/software/bin/GenomeAnalysisTK.jar -T DepthOfCoverage -R /bioinfo/data/iGenomes/genome.fa -o gatk -I ../4D_S1_dedup.bam -ct 1 -ct 2 -ct 10 -ct 30 -ct 50 -ct 100 -L ../../../Agilent_ClearSeq_Inherited.v1.bed java -jar /bioinfo/software/packages/picard-2.9.2/picard.jar CollectHsMetrics I=../4D_S1_dedup.bam O=picard.metrics R=/bioinfo/data/iGenomes/genome.fa BI=../agilent.intervals TI=../agilent.intervals MQ=0 Q=0
agilent.intervals was obtained by PICARD
java -jar /bioinfo/software/packages/picard-2.9.2/picard.jar BedToIntervalList I=Agilent_ClearSeq_Inherited.v1.bed O=Agilent_ClearSeq_Inherited.v1.interval SD=/bioinfo/data/iGenomes/genome.dict