Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!

picard of CollectVariantCallingMetrics error

[Thu Jun 29 17:13:02 CST 2017] picard.vcf.CollectVariantCallingMetrics INPUT=BGIyaozu.qc.vcf OUTPUT=BGIyaozu DBSNP=dbsnp_138.hg19.vcf GVCF_INPUT=false THREAD_COUNT=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Thu Jun 29 17:13:02 CST 2017] Executing as [email protected] on Linux 3.10.0-229.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0-b132; Picard version: 2.8.0-SNAPSHOT
INFO 2017-06-29 17:13:02 CollectVariantCallingMetrics Loading dbSNP file ...
[Thu Jun 29 17:13:02 CST 2017] picard.vcf.CollectVariantCallingMetrics done. Elapsed time: 0.00 minutes.
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.NullPointerException
at picard.util.DbSnpBitSetUtil.loadVcf(DbSnpBitSetUtil.java:163)
at picard.util.DbSnpBitSetUtil.createSnpAndIndelBitSets(DbSnpBitSetUtil.java:131)
at picard.vcf.CollectVariantCallingMetrics.doWork(CollectVariantCallingMetrics.java:105)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)


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