GATK best pratices for RNA-seq somatic mutation finding
Dear All, I have followed GATK best practices for finding Somatic mutations from cancer versus normal sample from RNA-seq data using Mutect2 as the final caller and rest all quality control steps as...
View ArticleWhat input files does the GATK accept / require?
All analyses done with the GATK typically involve several (though not necessarily all) of the following inputs: Reference genome sequence Sequencing reads Intervals of interest Reference-ordered data...
View ArticleError in AnalyzeCovariates
hi when i ran AnalyzeCovariates to visualize base recalibration results, i get below error. RScript exited with 1. Run with -l DEBUG for more info. how can i fixed that?
View ArticleVariantRecalibrator：ERROR MESSAGE: Bad input: Values for MQRankSum annotation...
I follow the best practice, use the haplottypecaller to call the variants, so I get a VCF file, but when I do the VQSR VQSR parameters same as best practice: -jar ~/biosoft/GATK/GenomeAnalysisTK.jar -T...
View Article[ERROR] Malformed VCF: empty alleles are not permitted in VCF records
I am running BaseRecalibrator for my RNA-seq: java -jar -Xmx120g ${GATK} -T BaseRecalibrator -R "${reference}" -I "${file4}" -knownSites "${gerVar}" -knownSites "${somVar}" -o...
View Article(howto) Test your GATK installation
Objective Test that the GATK is correctly installed, and that the supporting tools like Java are in your path. Prerequisites Basic familiarity with the command-line environment Understand what is a...
View ArticleCombineVariants - duplicate reads are generated for the same chr:pos
I am merging two VCFs. the records are as below VCF1: CHROM POS ID REF ALT QUAL 1 1247578 . TG TGG,TGGG,TGGGG,TGGGGG,T,TGGGGGG 53367.32 VCF2: CHROM POS ID REF ALT QUAL 1 1247578 . TG...
View ArticleBamout file shows a consistent deletion that is not reported in VCF
Dear GATK team I ran HaplotypeCaller on a bam file, which is the alignment of a single bacteria sample to its reference genome. To understand the calling process I wanted to compare the resulting VCF...
View ArticleMutect2 parallel problem
Dear GATK team. I am using Mutect2 to call somatic mutation from tumor/normal paired sample. However after jobs running for 8 days, our server has been rebooted for some reason. Most of the jobs are...
View Articlesomatic variant calling with no germline sample
Dear all, please could you advise : what is the best strategy to call the somatic variants in the absence of germline sample (when only the tumor sample is available) ? thank you, -- bogdan
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BroadE Workshop 2015 March 19-20: Best Practices for Variant Calling with the...
The full GATK team presented this workshop at the Broad Institute with support form the BroadE education program. This workshop covered the core steps involved in calling variants with the Broad’s...
View Article2017 Feb workshop presentation slides and tutorial materials
These are the materials that we are presenting at the February 2017 GATK workshop in Leuven, Belgium. Materials Link DAY 1: GATK Best Practices talks Slide decks presented on Day 1 Google Drive Folder...
View ArticleMergeSamFiles query
Hi, I used MergeSamFiles from Picard 1.141 (as it is currently installed in my server). Then I checked Picard website and came to know that 2.9.0 is currently available and I downloaded that. Do I need...
View ArticleTrio analysis using the GATK toolbox
While I am following the Best Practices documents, I started to get confused about the best sequence of steps to follow, after calling the common VCF file of the child, and parents. Some steps seem not...
View ArticleCompiling GATK-Lite from Github
I'm trying to compile and get GATK-Lite (free for all uses) to run. https://github.com/broadgsa/gatk After running "mvn verify" as well as "mvn clean install" and I get what appears to be successful...
View ArticleProblem: while converting vcf to plink file format?
java -jar GenomeAnalysisTK.jar -T VariantsToBinaryPed -R chr20_NOPREFIX.fa -V chr20.vcf -m chr20_NOPREFIX.interval_list -bed chr20.bed -bim chr20.bim -fam chr20.fam -mgq 0 Following above given command...
View ArticlePicard getting stuck at "Traversing read pair information and detecting...
Hello GATK team, I am using picard version 1.125, to mark duplicates on a BAM file. Here is my command line. /usr/bin/java -Xmx16g...
View ArticleOxoGmetrics task in GATK not found
Hello, I am trying run the OxoGMetrics task according to the following command (which I found in the Firehose task registry): java -Xmx2g -jar /GenomeAnalysisTK.jar --analysis_type OxoGMetrics -R -I -L...
View ArticleMutect2 with lastest nightly build problem
Hi, I am trying to run the variant calling step for the first time as a test. As I don't have any matched normal, I have only my tumour .bam file and a PoN composed of only 2 samples (for now). So I...
View Articlejava.lang.NullPointerException for Picard SamToFastq OUTPUT_PER_RG=T on bam...
Hello, When running Picard's SamToFastq with OUTPUT_PER_RG=T on a bam file without read group information, you get the following error: Exception in thread "main" java.lang.NullPointerException at...
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