How do I resolve the log4j errors while running BaseRecalibratorSpark using...
These are the errors: log4j:ERROR A "org.apache.log4j.ConsoleAppender" object is not assignable to a "org.apache.log4j.Appender" variable. log4j:ERROR The class "org.apache.log4j.Appender" was loaded...
View ArticleWhy "NO_READS" from DiagnoseTargets despite lots of reads in interval?
I a m running DiagnoseTargets on a list of intervals corresponding to targeted exons. In the result file, intervals are filtered by i.e. PASS, LOW_COVERAGE, COVERAGE_GAPS or NO_READS for each sample as...
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Understanding and adapting the generic hard-filtering recommendations
This document aims to provide insight into the logic of the generic hard-filtering recommendations that we provide as a substitute for VQSR. Hopefully it will also serve as a guide for adapting these...
View ArticleWhat's the difference between b37 and hg19 resources?
Hi, all. I have questions on resource bundles. Are the 'hg19' bundle files just liftover from 'b37' bundles in UCSC-style? If so, why are there some variants in only one version and not the other? For...
View ArticleHow do I produce a file with genotyping data admixture can use?
I have had my whole genome sequenced by Veritas and they have provided VCF.GZ and BAM files with the data. I'm wanting to run it with the 1000 Genomes data in admixture. So I downloaded the...
View ArticleBQSR with MuTect2: use it or not ?
Hello, I've been reading some threads on the forum about BQSR with MuTect2. I know it has been proposed in Best-Practices uses. However, there were a lot of mixed comments and I can't find a clear...
View ArticleProblem with joint genotyping
Dear Team, I am running joint calling (according to Best Practices). I have ~800 samples from 3 different centres.First I run CombineGVCFs on cases from batch1(~130samples), controls from...
View ArticleCannot find HaplotypeCaller
I downloaded GATK and ran the script. It gave this bizarre error where it couldn't find HaplotypeCaller. So I downloaded GATK again. I am still having the same error. Here is my input: java -jar...
View ArticleError: Argument with name 'drf' isn't defined.
Hello, I'm currently trying to call SNP on several samples (8 bam, 1 pseudoref) and 75.15% of my reads have failed the DuplicateReadFilter. I tried to disable this filter with "-drf DuplicateRead" in...
View ArticleCollectHSmetrics
Hi everyone, Thank you in advance for reading this. Has anyone else had the following problem when running CollectHSmetrics: [Tue Apr 12 12:17:52 EDT 2016] picard.analysis.directed.CollectHsMetrics...
View ArticleError running haplotypecaller (v3.3)
I am running the haplotypecaller on multiple samples all but one work correctly with the following commands, however one is resulting in a binary file instead of the gvcf. Any suggestions how to fix...
View ArticleMutect2 gets different results when I change the downsample level
I use mutect2 of GATK 3.6 and GATK 3.7 to call variant. I know there is a downsampling in mutect2 which has an important influence on the result. So I change the downsampling level. For example: the...
View ArticleMangrove charcoal Saudi Arabia
Mangrove Charcoal is one among the hardwood charcoals and also one among the heaviest charcoals. In other words, its structure is extremely dense and also exhausting. This charcoal is used for BBQ in...
View ArticleVariantAnnotator error with Freebayes merge: Must initialize the cache of...
Main question (for the community): How to solve / avoid getting the error Must initialize the cache of allele anyploid indices for ploidy 1 with the VariantAnnotator (3.7-0) and freebayes1.1.0 . The...
View Articleneed GenePattern modules for the latest Picard tools
(repost of part of a mail to Picard team) Is there someone out there having new GP modules for as many as possible Picard.jar subcommands (I love them all) I am preparing a variant training for the...
View ArticleERROR stack trace java.lang.NumberFormatException: For input string: "44.00"
Hi there ! I'm having the following error message (see below) when using VariantFiltration (GATK version 3.7.0). I have used this same code before without having any trouble. Any help welcome ! I'm...
View ArticleGATK ver. 2.7
I'm trying to run an older bacterial phylogenetic pipeline that was validated with GATK ver. 2.7. I have found documentation on this version, but not a link for download. Are older versions of GATK...
View Article(howto) Apply hard filters to a call set
Objective Apply hard filters to a variant callset that is too small for VQSR or for which truth/training sets are not available. Caveat This document is intended to illustrate how to compose and run...
View ArticleBAM problem prevents a fix_misencoded_quality_scores step
I ran the following code: java -Xmx100g -jar /work/reecygroup/GATK/GenomeAnalysisTK.jar \ -T BaseRecalibrator --unsafe -nct 16 \ -R /work/reecygroup/index/bos_taurus/bos_taurus_all_dna.fa \ -I...
View ArticleGATK4: execution stops with display of a cartoon
Apologies if this has been asked and answered. I don't even know how to frame a search of the forum for this. I'm running the GenomeAnalysisTk-4_1.jar. After the run of any GATK4 tool (even just...
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