Help me check my picard style intervals list file.
Hello, I used BedToIntervalList to convert bed file to interval list file. My intervals list file: ``` @SQ SN:chr18_gl000207_random LN:4262 M5:f3814841f1939d3ca19072d9e89f3fd7...
View ArticleGATK4,Cann't get right CalculateContamination result
Question regarding CalculateContamination(GATK/4.1.2.0): With CalculateContamination in tumor matched mode, I get: contamination error NaN 1.0 When I look at the tumor.table and normal. table files...
View ArticleInbreedingCoeff in VCF not matching my calculation
Initially I was going to ask about why I might be seeing some InbreedingCoeff values less than -1 (based on the calculation as explained at...
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Do you ever get frustrated by the current state of the GATK documentation? Do you find it hard to find information about what tools you should use and how they work? And when you do find relevant...
View ArticleCNNScoreVariants Running to end but failing to create a filtered file
Hi, I am trying to run CNNScoreVariants on an exome using: java -jar $GATK CNNScoreVariants -V ERR000589.raw.vcf -R $REFERENCE -O ERR000589.CNN.vcf I have a bam file, aligned with BWA with read headers...
View Article(How to) Call somatic mutations using GATK4 Mutect2
This tutorial is applicable to Mutect2 version 4.1.1.0 and higher. Post suggestions/questions in the Ask the GATK team section. GATK 4.1.1.0 contains several major advances in the Mutect2 pipeline,...
View ArticleTechnical support request: SortAndFixTags Failiure
Hello, My FireCloud analysis using method PreProcessingForVariantDiscovery_GATK4 (copied from Method repository: Snapshot 8), keeps failing during the SoftAndFixTags.log step. Failure seems to be due...
View ArticleWeb-based Oncotator server
There is a web-based version of Oncotator which you can use for annotation without running anything on your own machine. However, please note that the web-based version is an older version, with fewer...
View ArticleError messages when running StructuralVariationDiscoveryPipelineSpark
Dear GATK developers, I am running the following command to perform SV calling with StructuralVariationDiscoveryPipelineSpark: nohup /home/simone/software/gatk-4.0.3.0/gatk --java-options -Xmx100G...
View Articlevalue of joint genotyping in trio's
Hi, We're looking into modernizing our workflows and I was wondering if there's much value to joint genotyping very small cohorts (e.g. trio's), as opposed to comparing results of three separate...
View ArticleGATK4.0.9.0 undetected a delins site
Dear GATK team, I use GATK4.0.9.0 Haplotypercaller to detect germline variation, and find a delins site is not call. As the figure show, this is gvcf output, 32944606 is delTTT, and 32944609 is...
View ArticleErrors when I run the BaseRecalibrator
Hi,I got some errors when I used BaseRecalibrator. My GATK version is 4.1.2.0
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Somatic short variant discovery (SNVs + Indels)
Purpose Identify somatic short variants (SNVs and Indels) in one or more tumor samples from a single individual, with or without a matched normal sample. Reference Implementations Pipeline Summary...
View ArticleIssues on FilterMutectCalls: Log10-probability must be 0 or less
When I use FilterMutectCalls to Filter VCF resutls called by Mutect2, I got "Log10-probability must be 0 or less" Error on some of the VCF results (not all of them got the error message, maybe 10 out...
View ArticlePathSeq running too slow
Hi, I am trying to run PathSeq pipeline on single end RNAseq data (2.37GB unaligned BAM file). The pipeline is still running after 3 days. Below is the snapshot of the log file of the step that is...
View ArticleError using VariantAnnotator -A PossibleDeNovo
Hello there, I am trying too annotate novel variants. I have a VCF file containing a single trio family. I have run CalculateGenotypePosteriors on my file with no problems. I ran this with GATK4. I...
View Article(richardhanks99@gmail.com) Buy Registered IELTS,TOEFL,PTE,GMAT...
Buy Authentic IELTS, TOEFL, Certificates, Passports, Drivers License,ID Cards,Visas,Counterfeit Money,$,€ ... (richardhanks99@gmail.com) We provide registered IELTS,TOEFL,PTE,GMAT...
View ArticleIntroduction to the GATK Best Practices workflows
This article is part of the Best Practices documentation. See http://www.broadinstitute.org/gatk/guide/best-practices for the full documentation set. The "GATK Best Practices" are workflow descriptions...
View ArticleSortVcf
The order of file Mills_and_1000G_gold_standard.indels.hg38.vcf is not same with my genome fasta file,so I need to reorder it,I use SortVcf to do it.Before I run it,I run UpdateVcfSequenceDictionary...
View ArticleUse mutect2 or UnifiedGenotyper?
Hi, I am currently working on finding the somatic mutations in the tumor (using the sing cell sequencing result). And my final goal is to use these somatic mutations from different regions to build...
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