If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

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.

help with picard CollectHsMetrics

I tried to run CollectHsMetrics with this command

java -jar /picard.jar CollectHsMetrics \
I=190.sortedDeDup.bam \
O=190_hs_metrics.txt \
R=ucsc.hg19.fasta \
BAIT_INTERVALS=AgilentSSV6_bait_list.interval_list \

it works ok until minute 2, when it stops and display this error:
[Wed Dec 06 19:23:49 CST 2017] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 2.74 minutes.
To get help, see
Exception in thread "main" java.lang.IllegalStateException: Could not find percentile: 0.2
at htsjdk.samtools.util.Histogram.getPercentile(
at picard.analysis.directed.TargetMetricsCollector$PerUnitTargetMetricCollector.calculateTargetCoverageMetrics(
at picard.analysis.directed.TargetMetricsCollector$PerUnitTargetMetricCollector.finish(
at picard.metrics.MultiLevelCollector$AllReadsDistributor.finish(
at picard.metrics.MultiLevelCollector.finish(
at picard.analysis.directed.CollectTargetedMetrics.doWork(
at picard.cmdline.CommandLineProgram.instanceMain(
at picard.cmdline.PicardCommandLine.instanceMain(
at picard.cmdline.PicardCommandLine.main(

What am I doing something wrong?

Thank you


Sign In or Register to comment.