Picard RevertSam java.nio.file.NoSuchFileException
Hi, I'm starting to process a set of bams following the best practices and beginning from bams that were processed by someone else. Thus, I'm attempting to generate unmapped BAMs following this post,...
View Articleerror with VariantRecalibrator java.lang.IllegalArgumentException: No data...
Dear GATK Team, I have one whole genome data called with the HaplotypeCaller. I would like to apply the VariantRecalibrator to recalibrate my variant set, but I get back an error as follows: INFO...
View ArticleError in SortVcf
I have been going through this problem. Is this very common and is there any solution to this error. Exception in thread "main" java.lang.IllegalStateException: Key . found in VariantContext field INFO...
View ArticleGATK runtime error (READ_MAX_LENGTH must be > 0 but got 0) with 1000g bam
Hi, I'm trying to build a pon with GATK 3.7-0 to use with mutect2. For that, I've downloaded 80 exome bam files from the 1000g project (GBR, TSI, IBS and CEU populations). For most of them, when I try...
View ArticleGATK4: How to reassign STAR mapping quality from 255 to 60 with SplitNCigarReads
Hi, How can I reassign STAR mapping quality from 255 to 60 with SplitNCigarReads? In GATK 3.X this used to be done like this: java -jar GenomeAnalysisTK.jar -T SplitNCigarReads -R ref.fasta -I...
View ArticleX Chromosome gentyping
Now that GATK supports ploidy, how do people generate ChrX calls. My first guess is to have 2 separate genotyping runs, one for males with ploidy=1 and a second for females only with ploidy=2?
View ArticleDocumentation error in RNAseq workflow
We discovered today that we made an error in the documentation article that describes the RNAseq Best Practices workflow. The error is not critical but is likely to cause an increased rate of False...
View ArticleUnusually long runtime of Unified Genotyper?
Dear GATK-team I recently started my PhD and I'm working with large Illumina datasets (250-300mio Hiseq 150bp paired end reads) of pooled samples (10-12 genomes/pool). After the alignment against a...
View ArticleSNP calling for Cell lines - how does the ploidy affect HC
Hi all, I am calling SNPs in various immortalised cell lines, which are known to be very instable - hence the ploidy is not known. Generally it should be diploid. So my question is - what can happen if...
View Article(howto) Run the genotype refinement workflow
Overview This tutorial describes step-by-step instruction for applying the Genotype Refinement workflow (described in this method article) to your data. Step 1: Derive posterior probabilities of...
View ArticleVariantRecalibrator - no data found(run on one WGS sample)
hi, version:gatk-4.beta.4 I am trying to run VariantRecalibrator per WGS sample.Most samples done successfully.But a few of samples have identical error message"no data found".How can I fix command...
View Article[ERROR] CreatePanelOfNormals
I am trying to use CreatePanelOfNormals for build a PoN. java -Xmx128g -Djava.library.path=/usr/lib/jni/ -jar /root/gatk-protected.jar CreatePanelOfNormals -I...
View ArticleGenotype calls in PhaseByTransmission output VCF
Hello, I ran PhaseByTransmission (GATK ver 3.6) on trios to get a list of Mendelian violations. In the first run, we used BAMs at average coverage of ~100x and in the second run, we used down-sampled...
View ArticleWhat causes BaseRecalibratorSpark to run for a long time and end up failing...
Hi, GATK team, I am testing BaseRecalibrator in GATK 4.5 beta, when running in LOCAL mode, it finishes pretty fast. However when i run BaseRecalibratorSpark in SPARK mode, it runs for a long time and...
View Articlegoing to buy g4wow Outland gold
achievement, yet Shani the individual that was dependent on "Universe of Warcraft," hanging out with my day ones, going out and getting a charge out of life, everything! Appreciate and until next...
View ArticleValidateVariants Error on low coverage WGS variant calling
Dear GATK Team, first of all.. Thanks for the great work I love your software package. I am currently experiencing some problems on a low-coverage sequencing project. In a nutshell: We deep-sequenced...
View Articlegatk VariantRecalibrator used to work : adding more samples returns "No data...
Hi, gatk VariantRecalibrator (v3.7) used to work on my WGS data (about 600 samples) . I've added 100 more samples (via .gvcf) to my data set and now I've got a No data found. I'm just surprised that I...
View ArticleTraining set
Hello Geraldine! Great workshop in Huntington. Would you please give me a link to that training set you mentioned? Best Regards!
View ArticleCongratulations on the paper in bioarchiv and following up on "curious zero...
Hello Geraldine: Just scanned the ms and could not conclude if the old "bug" of contention is squashed in the latest version. Can you tell if the base quality surrounding small indels is now close to...
View Article--sparkMaster yarn failed: org.apache.spark.SparkException: Could not parse...
Hi all, I tried to play with the GATK4 on our Spark cluster. I tried the PrintReadsSpark with --sparkMaster yarn but was given following error: 17/11/22 13:41:44 ERROR SparkContext: Error initializing...
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