RevertSam Exception: File too large
When running RevertSam (4.0.1.2), I get the following "File to large" error. The bam file is only 109GB. Any suggestions? gatk --java-options "-Djava.io.tmpdir=tmp -Xmx64G" RevertSam\ -I $BAM_FILE \ -O...
View ArticleNoSuchFileException during running JointGenotyping locally
Dear GATK developers, I have a consistent problem when running the joint-discovery part of your gatk4-germline-snps-indels workflow. Independent of the file(path) I get a NoSuchFileException which...
View ArticleJava heap size error after Haplotypecaller finished traversal
Hi, This is strange and I am not sure if it has affected my gvcf file in any way or not, but I got the java heap size error after the traversal got over: 02:05:31.559 INFO ProgressMeter - Traversal...
View ArticleError: Unable to retrieve result, with "VariantRecalibrator"
My command lines are as following: java -Xmx8g -jar $CLASSPATH/GenomeAnalysisTK.jar \ -T VariantRecalibrator \ -R $GenomeReference \ -input $InputVCF \ -nt 6 \...
View ArticleGatherVcfsCloud in GATK v4.0.1.0 docker container returns Unable to parse...
Hello, I'm trying to merge some GVCF files from WES data. After making a hard filtering step, the GatherVcfsCloud command in GATK 4.0.1.0 docker image returns the following error stating that it can...
View ArticleTrouble with running GenomicsDBImport
I'm writing a pipeline using GATK4 for our local cluster which uses Slurm as job scheduler. The command below seems to run successfully, however, it took only a few seconds and the output file sizes...
View ArticleMutect2 AF calculation discrepancies
Hi, I called some targeted DNA-seq using GATK 4.0 mutect2 : java -jar $gatk_jar Mutect2 \ -R $ref_fasta \ -I $bam \ -tumor $sample \ -L $genomic_interval_bed \ --dbsnp $dbSNP_vcf \ -O...
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Error in GatherBQSRReports
Hi, starting from WES pair-end data... in the BaseRecalibrator step I used as interval these regions/chr: chr1-22, chrX, chrY, chrM, alternative contings and HLA contings. In the case of HLAname I...
View ArticleGatherBamFiles / FixMateInformation / ValidateSamFile
Hi, here the pipe... 1) ApplyBQSR while read -r f1 f2; do .... ${ph6} --java-options ${java_opt1} ApplyBQSR -R ${gnm} -I ${fBAM} -O ${fol5}/${c_applybqsr} -L ${f1} -bqsr ${fol5}/${bqsrrd}...
View ArticleI can't run GATK4 BwaSpark tool on a yarn cluster
I am trying to run the gatk BwaSpark tool on Microsoft Azure cloud, by issuing the following command (Note that I am a bit unsure about how many / should I put with hdfs:. If my file is in...
View Articlehandcurated.20k.intervals
Hi, where can I find and download this list: JointGenotyping.unpadded_intervals_file: "gs://gatk-test-data/intervals/hg38.even.handcurated.20k.intervals" All the best
View ArticleWhy this command in invailed? (CombineVariants PRIORITIZE)
Hi Sorry this may be a simple error but I could not find what's wrong 1108% [x1477lsj@tachyon3199 cell2012]$ /home01/x1477lsj/program/jdk1.8.0_131/bin/java -Xmx3g -jar...
View ArticleDiskReadEndsMap error
hello,I run a batch of markdup for mary samples on a servers, echo sample's script likes below: java -Djava.io.tmpdir=/tmp/17S0001690 -jar MarkDuplicates.jar MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000...
View ArticleHaplotypeCaller does not filter duplicate reads, why?
Hi, Im running HaplotypeCaller on a server this way: java -XX:ParallelGCThreads=8 -Xmx80g -jar $GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -I a2tl1_14_final.bam --min_base_quality_score 25...
View ArticleMutect2 equivalent of ReadPosRankSum?
Hi there, is there an equivalent ReadPosRankSum flag for Mutect2? I know there used to be a --pir_median_threshold flag that was similer(ish) but it seems to be gone. Is there a way to see if alternate...
View ArticleBatch effects begone: Introducing the Functional Equivalence data processing...
By Eric Banks, Director, Data Sciences Platform and original member of the GATK development team Ever since the GATK started getting noticed by the research community (mainly as a result of our...
View ArticleGATK4.0 does not have the any more
I wander why the mulitple thread parameter [-nt ] has been cancer in GATK4.0? Or GATK 4.0 use a better way to replace the mulitple threads process, like using Spark?
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CombineGVCFs: After combining 3 GVCF file, some information has losed.
Hi, When I used GATK4.0 CombineGVCFs to combine 3-sample GVCF file into a multi-sample GVCF file, a lot of information didn't preasent. As the three pictures present, the size of every file is greater...
View ArticleBuild Error in Mutect: GATK-Framework
Hi everyone, I am trying to install mutect on a Mac (El Capitan). The command mvn -Ddisable.queue install Is throwing this error message and I'd need you help here. [INFO] 5 warnings [INFO]...
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Off-label workflow to simply call differences in two samples
Given my years as a biochemist, if given two samples to compare, my first impulse is to want to know what are the functional differences, i.e. differences in proteins expressed between the two...
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