CNNScoreVariants, too much threads
Hi, in the BestPractice workflows you advise to use HaplotypeCaller with the "-XX:GCTimeLimit=50" and "-X:GCHeapFreeLimit=10" java options. Is there something similar for CNNScoreVariants? I tried to...
View ArticleMutect1 multi-allelic cases
Hello, We have worked hard to figure this out. By default, or by using any parameters, Mutect1 does not catch multi-allelic cases at a single position. It seems to pick one of the alternate alleles at...
View ArticleCreateReadCountPanelOfNormals in GATK4.1 doesn't output valid HDF5 files
Hi GATK team, I was testing somatic CNV workflow in GATK 4.1. I found that CreateReadCountPanelOfNormals doesn't output valid HDF5 files. As an example, I have generated HDF5 files from three normal...
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What are the requirements for running GATK?
Contents Skills / experience Input data Software Hardware 1. Skills / experience We aim to make the tools usable by everyone, regardless of your background. The GATK does not have a Graphical User...
View ArticleInstall with conda, gatkcondaenv.yml not found
This link from https://software.broadinstitute.org/gatk/documentation/article?id=11049 is dead and no link is present in https://software.broadinstitute.org/gatk/documentation/article?id=12836. Where...
View Article(How to) Install and use Conda for GATK4
Some tools in GATK4, like the gCNV pipeline and the new deep learning variant filtering tools, require extensive Python dependencies. To avoid having to worry about managing these dependencies, we...
View ArticleStrategies used by Genome Strip to detect CNVs
Dear all, I'm only want to know which strategies are used by Genome Strip in order to detect the CNVs... I looking for in the Genome Strip web page but I'm not sure... I saw in different papers where...
View ArticleJava related error encountered while running gatk PathSeqPipelineSpark
Hi, I am trying to test the pathseq tutorial following the tutorial on this link I ran the following commands bioinfo@bioinfo$ conda activate gatk (gatk) bioinfo@bioinfo$ gatk PathSeqPipelineSpark \...
View ArticleSomewhat off-topic: BroadE GATK4 workshop on Terra
On the events webpage there's an event called "BroadE GATK4 workshop on Terra", but I can't find any information on it at all. Is it an online workshop? Do you have to sign up? Didn't know a better...
View ArticleNew! Mutect2 for Mitochondrial Analysis
Overcoming barriers to understanding the mitochondrial genome Announcing a brand new “Best Practices” pipeline for calling SNPs and INDELs in the mitochondrial genome! Calling low VAF alleles (variant...
View ArticleVariantRecalibrator tranche plots have a lot of false positives
Hello! I am working with data from 122 human whole exomes, captured using SeqCap EZ Prime Exome. My software versions are GATK 3.8.0 and java 1.8.0_131. After following the Best Practices guidelines, I...
View ArticleError when running CNVDiscovery in a batch-like way: “Read count cache file...
Dear Genome STRiP users, I am running CNVDiscovery pipeline in a batch-like way, and always fail in No.4 batch, and No.23 batch with the following error: INFO 02:38:02,459 RefineCNVBoundaries -...
View ArticleError when running SVCNVDiscovery in batch-like way: Read count cache file is...
Dear Genome STRiP users, I am running SVCNVDiscovery process in a batch-like way. To be precisely, I have 3418 samples, and I divided them into 33 batches: the first 32 batches with 100 samples each...
View ArticleVCF and pedigree info
Hi, I have a trio WES data that I'm trying to run mendelian error rate with RTG tools. Following the GATK best practices, I ran BWA, SortSam, Marduplicates, BaseRecalibrator, BQSR, and HaplotypeCaller,...
View ArticleMutect2 allele specific stats for Multiallelic sites
Hello, I want to have allele specific stats for multi allelic sites. I was able to have this information by using other somatic variant callers, but I couldn’t get that info from neither mutect2 nor...
View ArticleFeedback on approach to create a custom truth set for VQSR
Hello! I would like to ask you for feedback on my approach to construct a truth set, since there is no such resource for my species. What I am doing is to: 1/ call variants with GATK best practices by...
View ArticleUsing CAVA-Annotated VCF file for VariantsToTable
Hi all, I have generated a VCF file via the 5 dollar genome analysis pipeline. Then I used a script called CAVA (https://tinyurl.com/y6bjhskc) to annotate the variants in my VCF file. CAVA added some...
View ArticleIntervals in Joint Discovery WDL
Hi folks. We are trying to use the sample Joint Discovery WDL on Terra/FireCloud for joint discovery of some canine gVCFs. I've had to make some edits to remove human-specific resources, but here's the...
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should BaseRecalibrator command add a bed file on wes or panel calling snv
https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.11.0/org_broadinstitute_hellbender_tools_walkers_bqsr_BaseRecalibrator.php so BQSR must supplied a bed file, am I right, thanks a lot...
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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...
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