java.lang.NullPointerException when running genotypeGVCF on >100 samples
After processing BAM, I made GVCF for each sample, and use genotypeGVCFs here. Running the following command in parallel mode (multi-threads) cases an error: /work/share/software/jre1.8.0_111/bin/java...
View ArticleAbout fastaalternatereferencemaker in GATK 4.0
Where is the fastaalternatereferencemaker in GATK4.0? I want to build a reference with mutation by fastaalternatereferencemaker, but I can not find the commond of fastaalternatereferencemaker , please...
View ArticleNo heterozygous variants after converting vcf file to fasta
Hello eveyone, Now I'm struggling with a problem that when I converted a vcf file to fasta, I found there was not any heterozygous variants in the fasta file which was unexpected to see. Below was my...
View ArticleStructuralVariationDiscoveryPipelineSpark Documentation
The StructuralVariationDiscoveryPipelineSpark requires the parameter --contig-sam-file. However, there is no description of the parameter in the input and the example code. Inputs An input file of...
View ArticleImpact on GATK performance due to Vulnerabilities - Meltdown and Spectre ?
Dear GATK Team, I developed an exome pipeline with standard GATK Best Practices guidelines (BWA-MEM align + Realign + BQSR + HaplotypeCaller). Our pipeline implements GATK 3.7 and it runs on a local...
View ArticleInconsistency between Alt Variant in BAM and bamout from MuTect2
I have a BAM from MarkDuplicates, Realigned and Recalibrated pipeline showing only 2 reads with deletion. After MuTect2 pipeline the somatic genotype shows 6 reads (marked below). I have only found 2...
View Articleusing multiple threads while running GATK4 on local server
Dear GATK Team, As GATK-4.0.0.0 released, and there are many new tools are also incorporated in this release. I wonder how to utilize the multiple thread options for GATK-4.0 and which tools are...
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FireCloud is listed as unverified
Google has just warned me about FireCloud being an unverified developer therefore incurs a security risk for my google account. I guess broad should straighten this up with google.
View Article[GATK4.0]Which steps should be done before 'ReadsPipelineSpark '?
In the latest version GATK4.0, the function of pipeline 'ReadsPipelineSpark ' is that Takes unaligned or aligned reads and runs BWA (if specified), MarkDuplicates, BQSR, and HaplotypeCaller to generate...
View ArticleNeed Fitness Tracker with Smart Watch
I'm looking for some advice and recommendations as I'm planning on buying one. I need to make some lifestyle changes again and think this will help me. Ok, so what do I want? Fitness Tracker?
View ArticleHaplotypeCaller in GATK4 vs GATK3
I know that HaplotypeCaller in GATK4 is still in development, but I want to make sure this issue is known We're seeing very different behaviour between the HC in GATK3 and GATK4 when using targeted...
View ArticlePicard liftoverVCF error when attempting to liftover to build 38
Hi, Apologies for the Biostars cross-posting, but haven't received any replies there yet, so was hoping for some help. I've been trying to lift over .vcf files (human) from build 37 to build 38 using...
View ArticleHelp! I have soooo many WARN in gatk4 HaplotypeCaller
Hi, I use gatk4 to call gvcf, but it is too slowly than gatk3.8, and have so many WARN. What should I do? Below is the command and stdout. [node1 whzhang:~]$ gatk-launch HaplotypeCaller -R...
View ArticleVariantsToBinaryPed java.lang.ArrayIndexOutOfBoundsException: -1
Hello, can you please help me sort out the following error in running VariantsToBinaryPed: java -jar /sb/project/fkr-592-aa/data/GalWaRat/bin/third/gatk-3.7/GenomeAnalysisTK.jar -T VariantsToBinaryPed...
View ArticleGATK best practices Short somatic variant calling: ExAC file
Hi, I was wondering if you could give some insight in the creation/preparation of the ExAC vcf file mentioned in the jason file (mutect2.exome.inputs.json) on Github...
View Articlewhat reads from original BAM are listed in mutect2 VCF-output?
Dear GATK team, I am sorry if my question is naive. After running mutect2 (version 4.2) what positions (AND corresponding reads) from the original bam-file are reported in the vcf file? all that passed...
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Somatic calling is not simply a difference between two callsets
To better understand what somatic calling entails, let's contrast it to germline calling. We delve into the technical details of what is the same and what is different between Mutect2 and...
View ArticlePadTargets and ConvertBedToTargetFile No Longer in the toolkit
Hello, I am trying to run somatic CNV caller from GATK4 on Firecloud. When I run task that call PadTargets and ConvertBedToTargetFile I am getting an error stating that these are invalid commands....
View Articlevisualize CNV results from WGS analysis
Dear all, please would you advise : what would be the best way to visualize the CNV that were predicted based on WHOLE-GENOME CANCER samples ? shall we upload in IGV both BAM files for TUMOR and...
View ArticleMaybe one code bug with GATK 3.7
@valentin @Geraldine_VdAuwera I had transform some code from JAVA to C in HaplotypeCaller step 2 ; CommonSuffixSplitter.java before if ( prefixV == null ) { // this node is entirely explained by suffix...
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