Help with BaitDepthWalker analysis
Hi, I am trying to get the coverage data using BaitDepthWalker tool: java -jar recapseg-1.4.4.0/coverage.jar -T BaitDepthWalker --input_file normal_aln_IndelRealigned_ReorderedSam.bam --intervals...
View ArticleMuTect2 Discards lots of reads?
MuTect2 discards 74.26% of the reads as below, becasue of 39% duplicate reads ans 34 % notprimary reads.Below is Star alignments we have higher mapping? And below is my commad, I don't have matched...
View ArticleExit codes in GATK 4.0
Hi, In my BASH scripts I often use "$?" to monitor the exit status of a process and normally stop if there is an error. However, I am using the latest version of GATK (4.0.0.0) and some tools return 0...
View ArticleError in GATK4 MUTECT2
Hello I am using RNASeq somatic mutations calls, using GATK I got this error in somatic mutation using GATK4 Mutect:: BAM header sample names [S1]does not contain given tumor sample name S1 This is how...
View ArticleChanging compression level in GATK 4.0.0.0
When running GATK 4.0.0.0, (in this case using Apply BQSR) the notice 11:36:10.430 INFO ApplyBQSR - HTSJDK Defaults.COMPRESSION_LEVEL : 1 appears. A bit of digging led me to the Python code in the...
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 ArticleUnable to load library 'lsf': liblsf.so and Unable to load library 'drmaa':...
I am running CNVDiscoveryPipeline and it is throwing following error Unable to load library 'lsf': liblsf.so. The command used is java -Xmx150g -cp ${classpath}...
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HaplotypeCaller may fail to detect variant with the same reads with a...
I have experienced a variant detection issue with confusion. The png file attached is the result of exact same NextSeq experiment but the read extraction range is different. NextSeq2_point.bam: bam is...
View ArticleRealignerTargetCreator ERROR MESSAGE: Invalid command line: Failed to load...
Hi, What does this error msg try to tell me? Is the 'reference dictionary' the refseq? If yes, why can't it load it (the file is OK, sourced from the bundle, successfully used with bwa and Picard)....
View ArticleGATK4 Variant Recalibrator not recognizing format of...
The following error is observed when running VariantRecalibrator with the --truth-sensitivity-tranche argument. A USER ERROR has occurred: Argument truth-sensitivity-tranche has a bad value: [100.0,....
View ArticleMutect2 (GATK4) annotations
Hi, I've encountered some issues when including annotations running Mutect2 in GATK4 (v4.0.1.2). My use-case is an unsupported feature of GATK4 (calling somatic variants without a matched normal...
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Calling variants on cohorts of samples using the HaplotypeCaller in GVCF mode
This document describes the new approach to joint variant discovery that is available in GATK versions 3.0 and above. For a more detailed discussion of why it's better to perform joint discovery, see...
View ArticleGATK4 CollectHsMetrics - How to avoid the overlap of adjacent intervals ?
Hello, I'm trying to access the quality of my targeted experiment, and I'm interested on saving the per target information using the --PER_TARGET_COVERAGE argument. However, I observed that when...
View ArticleDetecting called Indels with low read support on both sides?
Hi, I am mapping chimpanzee samples to the human reference hg19. I mappend the samples using the standard protocol (BWA mem, remove duplicates, indel realigner) and called them with GATK 3.7 Haplotype...
View ArticleCombining variants from different files into one
Solutions for combining variant callsets depending on purpose There are three main reasons why you might want to combine variants from different files into one, and the tool to use depends on what you...
View ArticleBQSR and False Negatives?
I am looking at GATK Best Practices for Data Processing and Germline Variant calling. I see that the workflow calls for base quality score recalibration using BaseRecalibrator...
View ArticleArrayIndexOutOfBoundsException error in BaseRecalibratorSpark
Hi, Thank you for your time. I ran BaseRecalibratorSpark with GATK4 and GATK4-protected on Amazon instance. Both of them gave me error java.lang.ArrayIndexOutOfBoundsException: 1073741865. When running...
View ArticleCombineGVCFs - All alleles are missing
Hi, I am combining gcvf files into single gvcf files by chromosome, using CombineGVCFs, in order to run GenotypeGVCFs. When I checked the first gvcf file generated by CombineGVCFs, I noticed that at...
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Seeing multiple calls for the same position
Hello, I am running a trio through the best practices pipeline for 3.7 and finding an unexpected result. I am seeing some positions that are being called multiple times with different calls. First, as...
View ArticleMINIMUM_GENOME_FRACTION - doesn't impact results on picard.jar...
I ran picard CollectGCBiasMetrics on 3 different bamfiles using 10 different settings creating a total of 30 plots. I found no difference between any of the results. MINIMUM_GENOME_FRACTION was set...
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