Different "java.lang.OutOfMemoryError: Java heap space" at nearly the end of...
Dear Genome STRiP users, I nearly completed the SVPreprocess to all 10686 samples: INFO 01:17:45,002 QGraph - 4 Pend, 2 Run, 0 Fail, 32076 Done However, I met a similar but not the same...
View ArticleBest Practices RNAseq Test Files
Hello GATK team, I've been using NA12878.bam as a test file for RNAseq short variant discovery workflow as stated in the inputs JSON file. After running the workflow, the portion of unmapped reads was...
View ArticleOut of order read after MarkDuplicateSpark + BaseRecalibrator/ApplyBQSR
Hi, I am building a workflow for discovery of somatic snvs + indels that is pretty much the Broad's Best Practice but incorporating MarkDuplicatesSpark and a couple of other minor changes. Today I was...
View ArticleHow is the phasing done in single sample HaplotypeCaller?
Hi, after running HaplotypeCaller with this commands gatk --java-options "-Xmx4g" HaplotypeCaller -R $refGenome -I /home/ready.bam -ERC GVCF -O /home/GATK4-HC.g.vcf I obtain positions in the gvcf file...
View ArticleGermlineCNVCaller, some samples do not have read depth metadata
GATK4.1.0.0, linux server, bash Hi, I'm testing the following commands: ${GATK4} --java-options "${javaOpt}" DetermineGermlineContigPloidy \ -L ${fol7}/"${INTERVAL}.preprocessed.interval_list" \...
View Articlegatk4 Mutect2 call vcf , is there a order of normal sample name and tumor...
I see a guide about how to use gatk4 mutect3, the order is normal first, is this a constant order, what is order of TAK3. if the order is tumor first, is there any bad consequence? thanks a lot.
View Articleis ther a depth limit in gatk4 ? if so, whether it means not suitable for...
is ther a depth limit in gatk4 ? if so, whether it means not suitable for deep depth? is there a concrete depth number
View ArticleCollectSequencingArtifactMetrics just need to work on tumor bam file
when do paired sample using gatk4 mutect2, dose CollectSequencingArtifactMetrics just need to work on tumor bam file
View ArticleClik here to view.
(How to) Call somatic mutations using GATK4 Mutect2
Post suggestions and read about updates in the Comments section. This tutorial introduces researchers to considerations in somatic short variant discovery using GATK4 Mutect2. Example data are based on...
View ArticleGATK4 pipeline in easy bash scripts, please
Hi, I asked this question a while ago and a few times. I know, there is a wonderful WDL platform and fire cloud stuff to run things in parallel and check this and that. But, for someone who are so used...
View ArticleSVCNVDiscovery Error "java.lang.OutOfMemoryError: Java heap space" AFTER...
Dear Genome STRiP users, I completed the SVPreprocess to the 10686 samples successfully. When I run SVCNVDiscovery pipeline with the following script,...
View ArticleSVCNVDiscovery Error: java.lang.RuntimeException: Read count cache file
Dear Genome STRiP users, I am running SVCNVDiscovery pipeline to 10686 samples with successfully completed SVPreprocesse. I met two "java.lang.RuntimeException" errors in the output. Exception in...
View ArticleVariantRecalibrator accepts only one VCF file?
The documentation on VariantRecalibrator reads: --variant -V [] One or more VCF files containing variants However, when I supply multiple VCF files I get this error message: A USER ERROR has occurred:...
View ArticleClik here to view.
LeftAlignAndTrimVariants --splitMultiallelics changes GT from known to unknown
I have a VCF file with this line (i.e. GT=0/1=G/T): 20 10120854 . G T,A 32175.56 . AC=399,18;AF=0.111,5.006e-03;AN=3596;BaseQRankSum=1...
View ArticleA problem met when running Mutect2 4.0.9.0
14:44:03.509 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 14.865818774000001 14:44:03.509 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 3144.705825942...
View ArticleGATK v4.1.0.0 ValidateVariants, gVCF mode, error; non in v4.0.11.0
GATK v4.0.11.0 & v4.1.0.0, linux server, bash Hi, I was running the following codes ${GATK4} --java-options '-Xmx10g -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:ConcGCThreads=1...
View ArticleCNNScoreVariants problem? Slow or stopped?
Dear all, I'm working trying to use CNN to annotate my VCF, adopting wdl from gatk4-cnn-variant-filter in GitHub (gatk-workflows) My project is a custom target capture panel and I've scattered my bams...
View ArticleParameters for running GenomicsDB import
I have a system with about 8GB RAM. I've run HaplotypeCaller (-ERC GVCF) on specific genes of my interest using a .list file and have 109 **.g.vcf.gzs **of about 5-10 GB each. What would be the most...
View Article(How to) Consolidate GVCFs for joint calling with GenotypeGVCFs
In GATK4, the GenotypeGVCFs tool can only take a single input i.e., 1) a single single-sample GVCF 2) a single multi-sample GVCF created by CombineGVCFs or 3) a GenomicsDB workspace created by...
View ArticleQuestion: Mutect v1 doesnt finds second alternative allele
mutect version 1 doesnt find any alternative allele than the first one. I use mutect 1 to find somatic variant calling. the reason i dont use mutect 2 is beacuse it produces too many false positives....
View Article