SplitNCigarReads error
I used SplitNCigarReads to split cigar, however I got this error: April 11, 2019 11:29:29 PM CST] org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads done. Elapsed time: 1.36 minutes....
View ArticleJava heap space
I performed GATK to call variants. but got this error: [April 13, 2019 5:24:50 AM CST] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 567.92 minutes....
View ArticleIs that "WARN DepthPerSampleHC and WARN StrandBiasBySample" normal ?
This is my all script: fa=/share/share/data/NGS/ref_index/GATK_bundle/hg38/Homo_sapiens_assembly38.fasta sample=P_4 bwa mem -t 6 -M -Y -R "@RG\tID:id_${sample}\tLB:human_lib\tPL:ILLUMINA\tSM:${sample}"...
View ArticleProblem with annovar
Hi, I faced a problem I am trying to annotate my `.vcf` files by `annovar` to get `maf` as by maf I am able to visualize and do many things. I tried both `vcf 4.1` and `4.2` [fi1d18@cyan01 annovar]$...
View ArticleGATK filter by minor allele frequency ?
I am reading a research paper that uses GATK to call variants and filtration. The method description goes: "In addition to the default filters in GATK, variants were further filtered for genotype...
View ArticleWhat does MuTect output means?
Hello! Currently, I am working on identification of somatic mutations on exome data. For this, I am using the combination of GATK + MuTect2 using following code: java -jar...
View ArticleAnalysis of somatic allele frequency
Good morning to all of you, We have used GATK4 Mutect 2 to call somatic mutations from a customised NGS panel. However, we have problems regarding the mutant-allele percentage given by Mutect2. As a...
View ArticleNot getting any output from GetPileupSummaries
Hi, I am getting GetPileupSummaries to complete seemingly without error. But, the output table has no records; it only has a header column. I have tried different steps to resolved, but I have not yet...
View ArticleERROR MESSAGE: Your input file has a malformed header
Hello, I want to annotate my file through gatk 3.8 but I get this error: MESSAGE: Your input file has a malformed header: there are not enough columns present in the header line: #CHROM POS ID REF ALT...
View ArticleMutect2 PoN for RNA-Seq
We're analyzing a batch of RNA samples to identify mutations. We don't have matched healthy tissue and we are wondering what would be the optimal panel of normals to use. We are thinking of using...
View ArticleGenomicsDBImport intervals and haplotaypecaller estimated time GATK 4.1.0.0
Hello, I'm trying to get VCF file following germline short variant discovery best practices. I have ready for variant discovery bam files. I have 2 questions: I need to specify time limit for jobs i...
View ArticleSelectVariants Cookbook
how to use SelectVariants to find common variants: gatk SelectVariants \ -V gs://gatk-tutorials/workshop_1702/variant_discovery/data/inputVcfs/trio.vcf.gz \ -select...
View ArticleGenotype (GT)
Hi all :) I have some doubts regarding the genotype. I don't understand: sample_AF is reflecting the GT, is it correct? I mean if AF is around 0,5 GT should be 0/1 and if AF is around 1 GT is 1/1. So...
View ArticleHow to add sample name column in Maf output from Funcotator?
First of all, I'd like to thank GATK team for providing brilliant software! I'm new to exome analysis and GATK. I'm analyzing ~10 tumor exome data using GATK4.1.1.0. I'd like to know how to add sample...
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Spanning or overlapping deletions (* allele)
We use the term spanning deletion or overlapping deletion to refer to a deletion that spans a position of interest. The presence of a spanning deletion affects how we can represent genotypes at any...
View ArticleGATKCombineGVCF produced truncated cohort.g.vcf file
I am trying to combine GVCF files from two different samples, run in intervals of 10000000 bases. It worked to get the Haplotypecaller GVCF file. I successfully also combined the two GVCF file in one...
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Germline short variant discovery (SNPs + Indels)
Purpose Identify germline short variants (SNPs and Indels) in one or more individuals to produce a joint callset in VCF format. Reference Implementations Pipeline Summary Notes Github FireCloud Prod*...
View ArticleEmpty FILTER column in Mutect2 output vcf - tumor-only mode
Hi, I have a question regarding Mutect2 output vcf. I am trying to run Mutect2 on paired-end reads (F and R reads for 1 sample at a time), tumor-only, sequenced by Illumina. I ran the following bash...
View ArticleInput for VQSR from Mergevcfs
Dear GATK staff, i have 28 vcf files from 31 humans exome data, the output after GenotypeGVCF according to the targeted gene intervals shows very little variant in each vcf files , less than 200 or 60...
View ArticleKnown sites for indel realignment and BQSR in hg38 bundle
Dear GATK team, I'd like to learn what files I should use for indel realignment and BQSR from hg38 bundle? (I read the manual on this topic -- https://broadinstitute.org/gatk/guide/article?id=1247 --...
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