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(How to part II) Sensitively detect copy ratio alterations and allelic segments
Document is currently under review and in BETA. It is incomplete and may contain inaccuracies. Expect changes to the content. This workflow is broken into two tutorials. You are currently on the second...
View ArticleCNV standardize and denoise plots disagree each other
Hi GATK Team, I'm following the CNV workflow: Sensitively detect copy ratio alterations and allelic segments. I ran step 1-4 with my own WGS 30x samples and a 7 sample PON to test against my tumor...
View ArticleGATK4 CNV ModelSegments hets output
Hi GATK team! I'm having trouble precisely understanding the ModelSegments hets output when ran on a tumor sample provided both a tumor and normal AllelicCounts are given. The documentation reads: If...
View ArticleCollected FAQs about interval lists
1. Can GATK tools be restricted to specific intervals instead of processing the entire reference? Absolutely. Just use the -L argument to provide the list of intervals you wish to run on. Or you can...
View ArticleMutect2 bamout depths not matching vcf.
Hi, After running Mutect2 on tumor/normal paired bam files, I get an output VCF with unusually high depth counts. I understand that the numbers here can differ from the input bam depths due to genotype...
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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 Article(howto) Get started with GATK4 beta
Download the software The GATK4 beta version command-line tools are provided as a single executable jar file. You can download a zipped package containing the jar file from this Github link (GATK4...
View ArticleAfter SplitNCigarReads, does the separated reads both labeled as primary...
Hi, I am doing RNAseq and use STAR for alignment, I am wondering in such situation, a read overlapping the junction site, when I use the SplitNCigarReads operation, it separate the read to two; for...
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Bug report: listing of workflow input display incorrect after first page.
In the monitor tab, when looking at workflow-level inputs and you need to page through the input, after the first page, the Task column shows the label name rather than the task name.
View ArticleRemoving variants based on the FORMAT field
Hi I have been trying to remove the Variants in my Sample with a GQ lower than 20 as part of the Genotype Refinement workflow java -jar GenomeAnalysisTK.jar -T VariantFiltration -R ref.fa -V...
View ArticleGATK v4.0.8.1 GenomicsDBImport Error (VariantStorageManagerException exception)
Hi, I am following the current best practice to prepare the consolidated GVCF from 5 samples of WGS for joint calling with the following command and encounter an error java -Djava.io.tmpdir=/work/TMP \...
View ArticleHaplotype Caller
This discussion was created from comments split from: New to the forum? Ask your questions here!.
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GATK4 VariantAnnotator
Hello, Has this tools been removed in the last release ? Thanks, Pedro
View ArticleGATK resource bundle
This discussion was created from comments split from: New to the forum? Ask your questions here!.
View ArticleFound contigs with the same name but different lengths; BQSR
This discussion was created from comments split from: Does the Broad still recommend aligning WXS/WES data to b37/hg19?.
View ArticleNormal-lod and tumor-lod in Mutect2
Hello, What are the normal-lod and tumor-lod in Mutect2? What are the bases of the default values 2.2 and 3.0 respectively? And, if the threshold are lowered or raised, what would be happened in terms...
View ArticleGATK4.alpha emitDroppedReads option
Does GATK4.alpha support -emitDroppedReads option that works with -bamout?
View ArticleMutect2 troubleshooting
I run Mutect2 in conjunction with a different variant caller and I try to keep the cutoffs as similar as possible. I don't expect the results to be identical. One caller might return twice as many...
View ArticleError when running oncotator
Hi, I installed Oncotator v1.8.0.0 on RHEL. I am getting following error when running the command oncotator -h Traceback (most recent call last): File "/usr/bin/oncotator", line 9, in...
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HaplotypeCaller may fail to detect variant with the same reads with a...
I have experienced a variant detection issue with confusion. The png file attached is the result of exact same NextSeq experiment but the read extraction range is different. NextSeq2_point.bam: bam is...
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