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GATK4.0.0.0 HCspark step run on spark cluster, -Unable to find _SUCCESS file
hello l tried to use the latest GATK version 4.0.0.0 on spark cluter,this step is HCspark .but I meet the question as follow the picture but when i can find it in my hdfs system,the result as follow...
View ArticleIllegalArgumentException: samples cannot be empty
I am trying to run HaplotypeCaller on some data that I know is messy and would fail some of the filters, so I have run it both with and without --disableToolDefaultReadFilters. Either way I don't get...
View ArticleIf I need to use SetNmMdAndUqTags?
I want to do snp calling and I have used MergeBamAlignment to merge ubam and bam files together with SORT_ORDER="unsorted". In this document I don't find any hint on SetNmMdAndUqTags. With this...
View ArticleIs it useful to call LeftAlignIndels after IndelRealigner
Hi, In my pipeline to find variants in bacterial genome, I am first calling IndelRealigner and then calling variants using HaplotypeCaller. As left aligning of indels seems to be an important step,...
View ArticleValues for indel qualities
Hi, I am a researcher from the Politecnico di Milano. I would like to ask a clarification about the indel qualities transition probabilites of the PairHMM in HaplotypeCaller. I am using some of your...
View ArticleFilterSAMReads ReadID pattern in Read_LIST_FILE
Hello, I am running FilterSamReads in picardtools with the following command: java -jar /bioinf/software/picard/picard-1.133/picard.jar FilterSamReads...
View Article-nct not present in GATK 4.0.0.0
Hi, Is --native-pair-hmm-threads in GATK 4.0.0.0 same as -nct in older GATK versions?
View ArticlePlease help for the very beginer--cannot build GATK4
Hello, I am very new unix learner. I use bash on Ubuntu on Windows10 I have downloaded and unzipped GATK-4.0.1.1, and gradle wrapper (latest version), java version:openJDK 1.8 when I run ./gradlew in...
View Article"CollectSequencingArtifactMetrics“ does not work
As we know, the function "CollectSequencingArtifactMetrics“ is necessary for remove artifact mutaitons before you do FilterByOrientationBias. However, I found an error in...
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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...
View ArticleCatVariant does not work.
Hi there, do you know why I got this error when I try to use CatVariant ? java -Xmx10G -jar /Users/xxx/bin/GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar org.broadinstitute.sting.tools.CatVariants \ -V...
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 ArticleWhen should I use -L to pass in a list of intervals?
The -L argument (short for --intervals) enables you to restrict your analysis to specific intervals instead of running over the whole genome. Using this argument can have important consequences for...
View ArticleQuestions about GenotypeVCFs output
Hi, I generated 12 .g.vcf files with HaplotypeCaller in GVCF mode and then a vcf with GenotypeGVCFs. What's the easiest way to split this vcf per sample ? Should I apply hard filtering first and then...
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 ArticleAbout SelectVariants
I want to filter out the variants if VAF in tumor samples was more than 0.3. Command line: gatk SelectVariants -V somatic_twofiltered.vcf -R ucsc.hg19.fasta -select...
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 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...
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Somatic short variant discovery (SNVs + Indels)
Purpose Identify somatic short variants (SNVs + Indels) in a tumor-normal for an individual sample. Requires an appropriate Panel of Normals (PON). Reference Implementations Pipeline Summary Notes...
View ArticleHow to create a coverage table for MutSig?
Hi, I am trying to use MutSig and would like to know if there is a way/script to generate coverage tables for the experiment under analysis. I have tried to use the standard exome_full192.coverage.txt...
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