Unknown index type error of SelectVariants
Good day to you! I ran a selectvariant command by nohup java -Xmx5g -jar /home/wuwei/software/GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar -R $referrence -T SelectVariants --variant:VCF...
View Article(How to) Run Spark-enabled GATK tools on a local multi-core machine
This is a placeholder for a document in progress.
View Article(How to) Run Spark-enabled GATK tools on a Spark cluster
This is a placeholder for documentation in progress.
View ArticleSpark
In a nutshell, Spark is a piece of software that GATK4 uses to do multithreading, which is a form of parallelization that allows a computer (or cluster of computers) to finish executing a task sooner....
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What are the smallest units I can break whole human genomes into, for...
Hi, and thank you so much for the wonderful tools and support! For our current project, we'd like to run 2000+ whole genomes from FASTQ to VCF using GATK best practices. I'd like to optimize the...
View ArticleHaplotypeCaller/ Variantannotator no allele balance tag for all SNPs
Version 3.1.1. Human normal samples. I couldnt find AlleleBalance and AlleleBalanceBySample tags in my vcf outputs. Tags are not found even for single variant I tried HaplotypeCaller with -all or...
View ArticleEstimation of the cross-individual contamination by chromosome
Dear all, We are trying to estimate the cross-individual contamination in our samples (whole genome) with ContEst and we were wondering if we could do it by chromosomes to speed up the process. We...
View Articleprebuilt gatk4 does not show --list on OSX HighSierra+java9
Hi there, Is it possible that mac and or java 9 are not happy with the gatk wrapper? Thanks in advance Stephane $ gatk --list Using GATK jar /opt/biotools/gatk-4.0.0.0/gatk-package-4.0.0.0-local.jar...
View ArticleOpen Tumor / Normal pair dataset for benchmarking and training
Hi, I am looking for a real tumor normal pair dataset to apply analysis and compare callers. Do you know of one I can get (bam would be quicker but even fastq is OK as I could map against 38 to be...
View ArticleInformation regarding the GATK Workshop in Taiwan
Hi, a colleague and I are quite interested in doing a GATK 4 training. Today I've seen the announcement in the event calendar that there is one of your larger trainings coming up in March in Taiwan. To...
View ArticleCombineGVCFs : key isn't defined in the VCFHeader
Hi there, I am trying to combine gVCFs using CombineGVCFs and get the error: "Key END found in VariantContext field INFO at chr1:10439 but this key isn't defined in the VCFHeader". The gVCFs are...
View ArticleTesting FPGA implementation of HaplotypeCaller (PairHMM)
Hi, We are two researchers from the Politecnico di Milano. We are trying to test the FPGA implementation of the HaplotypeCaller (PairHMM) on GATK 3.8-0-ge9d806836, using a Terasic DE5a-Net (Arria 10,...
View ArticleGATK4: CollectAlleleCount output & Model ModelSegments
Hi everyone, I am trying to run the CNV discovery pipeline and I have noticed that the header of sample.allelicCounts.tsv (produced by CollectAlleleCount) gives problems when used to rum ModelSegments....
View ArticleDynamically pass multiple input to Picard's MarkDuplicates (multiplexed data)
To pass multiple BAM files to MarkDuplicates we use the following syntax: java -jar picard.jar MarkDuplicates \ INPUT=lane1.bam \ INPUT=lane2.bam \ OUTPUT=dedup.bam \ METRICS_FILE=dedub_metrics.txt...
View Articlemerge bam files: dealing with alignment to a split reference database
Dear GATK team, I have a large reference database (NCBI nt) and it's to big to index. I split it to smaller partial dbs and run my alignment tool against each of the partial dbs separately. So for 1...
View ArticleIs there a consensus minimum number of probes to use as cutoff for GATK CNV...
Hello, I was just wondering if there was a cutoff used for the minimum number of probes that constitutes a segment. For example, there are a few segment calls made up of 2-3 probes that occur at a...
View ArticleDangling heads and tails
Hello, The logic for merging dangling tails appears to be different from that for dangling heads. For example, it looks like tails can be merged to a non-reference path while heads cannot. Is there a...
View ArticleSelectVariants error
I`m calling SNP by haplotype caller,and i got vcf document for each sample. After that , i use selectvariant to select variants of SNP . But i got this error: ##### ERROR...
View ArticleHow to call SNP without confidence SNP ？
Hello! I have WGS data of 100 samples. There's few people work on my species,so I didn't find confidence SNP set to use. I follow the best-practices of GATK. And my question is how to get convinced SNP...
View ArticleChanging compression level in GATK 4.0.0.0
When running GATK 4.0.0.0, (in this case using Apply BQSR) the notice 11:36:10.430 INFO ApplyBQSR - HTSJDK Defaults.COMPRESSION_LEVEL : 1 appears. A bit of digging led me to the Python code in the...
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