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Is it a bug for the Mutect2
Hi, I am using the Mutect2 (gatk-4.0.2.0) paired samples to call somatic mutation. Here is my command line: java -jar gatk-package-4.0.2.0-local.jar Mutect2 --reference hg19.fa -I...
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Strange behaviour (bias?) in BaseRecalibrator
Hello, I would like to report a possible weird behaviour of GATK BaseRecalibrator. During my analyses I follow the suggested "Best Practices", so after aligning I mark the duplicates (if needed) and...
View Articlehow to determine whether the variants is true by the IGV alignment views ?
Hi, how to determine whether the variants is true by the IGV alignment views ? is there a good paper to introduce that ? Best
View ArticleInput files known and reference have incompatible contigs
I have a question. I use the GATK RealignerTargetCreator, I have this error message. ERROR MESSAGE: Input files known and reference have incompatible contigs: Found contigs with the same name but...
View ArticleBWA parameters in gatk4-data-processing workflow
Dear GATK developers, I'm using the provided WDL script for data preprocessing (https://github.com/gatk-workflows/gatk4-data-processing). I noticed the BWA parameters are: bwa_commandline="bwa mem -K...
View ArticleReadBackedPhasing of somatic and germline variants?
Hi all, I'd like to know which germline variants are proximal to and on the same chromosome as detected somatic variants. Is there an out-of-the-box way to phase germline and somatic variants to one...
View Articlehard filtering one WGS raw.g.vcf
Hi, Im trying to apply hard filter to one WGS.g.vcf (coming form HaplotypeCaller). The command im using is: java -jar ${GATK}/GenomeAnalysisTK.jar -R ${reference}/mm10.fa -T SelectVariants -V...
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Inconsistent results with HaplotypeCaller on haploid organism
Hello GATK team, I would appreciate some help in understanding how GATK works in GVCF mode on my data. Here is my data example I'm usign GATK v3.8: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 328-16...
View ArticleMutect2 PON with one normal sample
I am trying to analyze several tumors and one normal with mutect2. They are not paired. Is it appropriate to use -I normal ? or create pon with one normal sample and use -pon option? Tried to use...
View ArticleWhy I obtained a g.vcf with wrong variant DPs, and too few variants according...
Hi, I extracted Exome regions from public bam files to apply the same pipeline that I did for my samples and merge them. It is weird that looking in the g.vcf files, I have very few "variants", and...
View Article-L option with PrintReads
I am using GATK-3.6 to analyze exome sequencing data. To speed up the analysis I split the BED file provided in GATK resource bundle (Broad.human.exome.b37.bed) into several files, one for each...
View ArticlePloidy level in HaplotypeCaller in GATK 4.0
Hi, Thanks for the new version of GATK (GATK4.0). We have a pooling of 48 samples and the organism is diploid, we are using ploidy of 96 (48x2=96). earlier when I am using HaplotypeCaller for variant...
View ArticleError in running variant recalibration
Hello, I am using GATK variant re calibration , it works fine on SNPs but throws an error on indel file. The error and my sample file are as follows: ERROR MESSAGE: Your input file has a malformed...
View ArticleGermline copy number variant discovery (CNVs)
Purpose Identify germline copy number variants. Diagram is not available Reference implementation is not available This workflow is in development; detailed documentation will be made available when...
View ArticleSeems Not The Right Genotype of My variants
Hello this is my GT:AD:DP:GQ:PL information of my variants : 0/1:4,42:46:11:1429,0,11 . It seems that "1/1" might the best genotype of my variant, can anybody tell me the reason. This is my command:...
View ArticleLet the GATK workshop season begin!
As I type this, four of my colleagues are kicking off a workshop in Taipei, hosted by Taiwan's National Applied Research Laboratories (NARLabs). For the next four days, they will be leading a cohort of...
View ArticleGATK4.0 HaplotypeCaller: Input files reference and reads have incompatible...
Hi， When I use GATK4.0 HaplotypeCaller, it present a similar errorA USER ERROR has occurred: **Input files reference and reads have incompatible contigs: Found contigs with the same name but different...
View ArticleWhat is the difference between ApplyRecalibration and ApplyVQSR
Hi, I am trying to do quality control for germline SNP & indels in 12 cancer patients. I have completed upto the VariantRecalibrator step. Now I am trying to figure out which tool do I use next...
View ArticleGATK ERROR MESSAGE: 38 HaplotipeCaller
Hello everyone, I´m using HaplotypeCaller program in whole sheep genome. The next paragraph is the command used for all 158 samples. We use nodes of 16 cores (-ntc 16) and 28 Gb of memory RAM. Could...
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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...
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