rules for max_alternate_alleles in HaplotypeCaller
Hi, I can't come to any clear conclusion how this parameter works. Help me, please. I worked on the same files with exact command but the max_alternate_alleles. In first command I put 1 for its...
View ArticleRead groups
There is no formal definition of what is a read group, but in practice, this term refers to a set of reads that were generated from a single run of a sequencing instrument. In the simple case where a...
View ArticleGermline VQSR recommended settings
Hi, we've been looking at the new Best Practices pages and at the WDLs linked there. In particular, we looked at the settings for VariantRecalibrator in this WDL. We ran germline analyses on samples...
View ArticleVCF index file corruption when using gatk-4.0.0.0
Recently, I noticed that the newest gatk release (4.0.0.0) is available now, so I just downloaded it for doing my jobs. However, when it came to BQSR steps, it returned messages including "Index file...
View ArticleGATK - 4.0.0.0 [BaseRecalibratorSpark low performance]
Dear GATK_team, I'd like to run Spark-enabled GATK tools on a Spark cluster. Precisely I am launching a Spark cluster in the standalone mode submitting the BaseRecalibratorSpark application via Slurm....
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(howto) Discover variants with GATK - A GATK Workshop Tutorial
GATK TUTORIAL :: Variant Discovery :: Worksheet June 2016 - GATK 3.6 This tutorial covers material taught at GATK workshops, and focuses on key steps of the GATK Best Practices for Germline SNP and...
View Articlebug with cat variants in both gatk37 and gatk38
I'm using gatk 3.7 I called variants using haplotype caller, and then extracted the non-variants and variants into seperate files so I could filter them seperately. I'm trying to merge them back...
View ArticleHow to parallelise HaplotypeCaller in 4.0.0?
Hello, At this time, what is the recommended way to parallelise HaplotypeCaller in GATK4, please? Assuming I care about results and don't want to use the Spark version. In particular, what is the...
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A USER ERROR has occurred: Bad input: BAM header sample names [LA4476D]does...
I have taken two samples(tumor-normal) from the same patient, with different names, when the mutect2 is excuted, it comes to such an error. how can i get through it? thanks!
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Genotype Refinement workflow
Overview This document describes the purpose and general principles of the Genotype Refinement workflow. For the mathematical details of the methods involved, please see the Genotype Refinement math...
View Articlemerge the output from SVgenotyper of genomestrip
Hello, I am running genometrip on genome sequencing data. i have 8 different varieties and i want to run genome strip for each species individually. after running the SVgenotype i got vcf file. Now,...
View Articlework flow for mouse SNP calling
Dear GATK team, Do you have any good article to follow the work-flow for mouse whole exome SNP calling. Is there inbuilt reference and annotation database for mouse in GATK? I would be really nice i...
View ArticleGATK 4 spark tools vs non-spark tools
Hi, I just started experimenting with GATK 4. In particular running through the spark tools (LOCAL). Am I missing something or is it not possible to go from spark tools for pre-processing...
View ArticleSNP Calling issue- Haptotype caller not calling all SNPs
Hi I am working with Candida albicans genome for SNP calling. Its Whole genome data. I used standard steps used here https://gencore.bio.nyu.edu/variant-calling-pipeline/ I am finding a very strange...
View Articlebypassing: "MESSAGE: Query asks for data past end of contig" error?
Hi, I'm running the following command as part of the rna-seq based variant detection pipeline: java -jar GenomeAnalysisTK.jar -T SplitNCigarReads -R target.fasta -I dedupped.bam -o splitNCigar.bam -rf...
View ArticleError MarkDuplicates (GATK4, Best Practices)
Hi! I'm trying to create the GATK4 pipeline but during the "MarkDuplicates" step I have the below error: CODE java -Dsamjdk.compression_level=${cl} -Xms5000m -jar ${ph3} MarkDuplicates...
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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...
View ArticleInvalid or corrupt jarfile
When I run ./gatk --help it seems to be working fine. However, running anything else such as ./gatk --list produces an error: Error: Invalid or corrupt jarfile...
View ArticleBuild Error: Java "unchecked conversion" error when building with gradle
Dear community, I have checked out a clean copy of the GATK4 repository (commit #4233). Now I am trying to compile the framework on my machine, which runs Mac OS X 10.13.2. I am in a conda environment...
View ArticleAvailabilty of Panels of Normals (PON)
Hi, Is the Panel of Normals (PON) vcf file publicly available now? The vcf file seems to be "wgs_hg19_125_cancer_blood_normal_panel.vcf" from the previous discussion...
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