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GATK on Alibaba Cloud
Alibaba Cloud, the largest cloud provider in China, has developed open-source command-line utilities that leverage Cromwell to enable execution of analysis pipelines on the Alibaba Cloud platform, as...
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GATK on Intel BIGstack for on-premises infrastructure
Broad-Intel Genomics Stack (BIGstack) is an end-to-end, optimized solution on Intel hardware for analyzing genomic data. It provides an efficient way to run pre-packaged, optimized workflows, including...
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GATK on FireCloud
FireCloud is an open platform for secure and scalable analysis on the cloud. More concretely, it's a web-based portal that is provided as a freely accessible service by the Broad Institute's Data...
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Germline short variant discovery (SNPs + Indels)
Purpose Identify germline short variants (SNPs and Indels) in one or more individuals to produce a joint callset in VCF format. Reference Implementations Pipeline Summary Notes Github FireCloud Prod*...
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Somatic short variant discovery (SNVs + Indels)
Purpose Identify somatic short variants (SNVs + Indels) in a tumor-normal for an individual sample. Requires an appropriate Panel of Normals (PON). Reference Implementations Pipeline Summary Notes...
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Somatic copy number variant discovery (CNVs)
Purpose Identify somatic copy number variant (CNVs) in a case sample. Requires an appropriate Panel of Normals (PON). Reference Implementations Pipeline Summary Notes Github FireCloud Somatic CNV case...
View ArticleGermline copy number variant discovery (CNVs)
Purpose Identify germline copy number variants. Diagram is not available Reference implementation is not available This workflow is in development; detailed documentation will be made available when...
View ArticleWhat is the FireCloud Free Credits Program?
The FireCloud Free Credits Program is an opportunity for you to use FireCloud, the Broad's cloud-based analysis portal, for trying out the new GATK4 Best Practices pipelines at no cost to you. All the...
View ArticleIntroduction to the GATK Best Practices
This document provides important context information about how the GATK Best Practices are developed and what are their limitations. Contents What are the GATK Best Practices? Analysis phases...
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RNAseq short variant discovery (SNPs + Indels)
Purpose Identify short variants (SNPs and Indels) in RNAseq data. Diagram is not available Reference Implementations Pipeline Summary Notes Github FireCloud RNAseq short variant per-sample calling BAM...
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Data pre-processing for variant discovery
Purpose The is the obligatory first phase that must precede all variant discovery. It involves pre-processing the raw sequence data (provided in FASTQ or uBAM format) to produce analysis-ready BAM...
View ArticleVQSR and VariantAnnotator on Samtools VCFs
Hi everyone! My goal is to run VQSR on VCFs generated with samtools mpileup. According to GATK best practices first i have to run VariantAnnotator on each of my VCFs in order to do that. here's the...
View ArticleOncotator output from 1.8 and 1.9
Are the 2 versions giving same output? The columns in the output files from the 2 versions are the same, right?
View ArticleUse Select Variants on a gnomAD vcf for Mutect2 contamination filtering.
I am trying to follow this set of steps to use the mutect2 wdl from the Broad. https://github.com/broadinstitute/gatk/tree/master/scripts/mutect2_wdl In that file, it is recommended to make a...
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Differences between HaplotypeCaller and Mutect2
They share graph assembly--similarities end there Operationally, Mutect2 works similarly to HaplotypeCaller in that they share the active region-based processing, assembly-based haplotype...
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Variant Quality Score Recalibration (VQSR)
This document describes what Variant Quality Score Recalibration (VQSR) is designed to do, and outlines how it works under the hood. The first section is a high-level overview aimed at non-specialists....
View ArticlePlot bqsr error using wdl.
Hi there, I keep getting hard link error during my plot_bqsr step using wdl. Any suggestion how to fix it? I tested the BQSR_1 and BQSR_2 both worked and on commandline I could run the...
View Articleexome hg38 interval list
Hi . GATK team! Please tell me if I am available exome interval list version hg38. -thanks
View ArticlePast National basketball association person
Past National basketball association person Lamar Odom particulars his or her struggle pertaining to sobriety, life's battles Odom covers their drug-fueled downfallLos Angeles Lakers7dESPN information...
View ArticleNine players acquire qualifying delivers because
Nine players acquire qualifying delivers because baseball’s free of charge agency interval will begin * SFGate Get SFGate news letters for that most up-to-date from your These kinds of...
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