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2. Special GATK Use Cases

Update The error has been solved by redownloading Mills_and_1000G_gold_standard.indels.hg38.vcf.gz(.tbi) but the error message is distracting anyway. -----------------------------------------------...

• WangZiwei
• January 05, 2022 09:44
• Edited
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1. Community
2. General Discussion

(REQUIRED) Please provide: a) GATK version used: 4.1.8.0b) Exact command used: example code in https://gatk.broadinstitute.org/hc/en-us/articles/360035890011  gatk --java-options "-Xmx3g" CollectAl...

• WangZiwei
• August 08, 2020 09:20
• Edited
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1. Community
2. Somatic

Sorry if I posted twice. I posted it again because the previous post was pending approval. Maybe I inserted too many links in it. Main Problem： Mutect2 PoN best practice pipeline executed with WDL+...

• WangZiwei
• August 07, 2020 07:21
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1. Community
2. Somatic

There are 2 wdl pipeline for mutation calling respectively in: https://github.com/broadinstitute/gatk/tree/master/scripts/ https://github.com/gatk-workflows/gatk4-somatic-snvs-indels They look diff...

• WangZiwei
• July 20, 2020 07:28
• 2 followers
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1. Community
2. Somatic

Can you please provide a) GATK version used （docker 4.1.8.0）b) Exact GATK commands used config=${bindir}/cromwell.mutect2.confcromwell_engine=${bindir}/cromwell-49.jarwdlscript=${bindir}/gatk4-soma...

• WangZiwei
• July 20, 2020 04:55
• Edited
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