How many "-an" arguments in VariantRecalibrator should be used ?
I encountered a problem when using VariantRecalibrator function of GATK. The following error often came out when I used the several common “-an” augments. “##### ERROR MESSAGE: Bad input: Found...
View ArticleMESSAGE: Unable to create iterator for rod named variant in GenotypeGVCFs
Hi all, I tried everything I can do, but can not find the solution. Any help will be appreciated. PROGRAM DETAILS: GATK version: GATK v3.6-0-g89b7209 Program Args: -T GenotypeGVCFs -D dbsnp_137.b37.vcf...
View Article(howto) Call variants with HaplotypeCaller
Objective Call variants on a single genome with the HaplotypeCaller, producing a raw (unfiltered) VCF. Caveat This is meant only for single-sample analysis. To analyze multiple samples, see the Best...
View ArticleGatk Variantannotator not reannotating old rsIDs
Hello Everyone, I am trying to reannotate some .vcf produced using the miSeq pipeline using dbSNP version 137. I am currently using VariantAnnotator to reannotate the called variants with the latest...
View ArticleOncotator data sources
For human / cancer-related research applications, we aggregate annotations from the following resources listed below. Please note that some of these may not be publicly available. We provide a bundle...
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(How to) Mark duplicates with MarkDuplicates or MarkDuplicatesWithMateCigar
This tutorial updates Tutorial#2799. Here we discuss two tools, MarkDuplicates and MarkDuplicatesWithMateCigar, that flag duplicates. We provide example data and example commands for you to follow...
View ArticleSingle-base deletion even after -selectType SNP?
I called SelectVariants in GATK 3.6-0 using the following command: java -jar ./gatk-3.6-0/GenomeAnalysisTK.jar -T SelectVariants -selectType SNP -V "DNA-level-vars.vcf" -o "DNA-level-vars.snpsonly.vcf"...
View ArticleInconsistent Calls by MuTect2
Hi, I have noticed a rather strange behavior by MuTect2. Running ten independent runs of MuTect2 on the same tumor/normal pair, I observe a variation in AF for some variants. It always seems to be...
View ArticlePICARD AlignmentSummaryMetrics
Hi I used the following command to gather summary metrics for my bam file generated via bowtie2 (tophat to be specific): java -jar /usr/share/picard-tools-1.136/picard.jar...
View ArticleConfiguration of GATK4 sparktools
Hi, I wondered if my local spark configurations, just as the settings in "spark-env.sh", matter with the performance of sparktools in GATK4, or if GATK4 brings along a set of spark parameters and...
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Spanning or overlapping deletions
We use the term spanning deletion or overlapping deletion to refer to a deletion that spans a position of interest. The presence of a spanning deletion affects how we can represent genotypes at any...
View ArticleMuTect2 seems to be hung, has created .vcf but run for many hours without...
I've had several instances of MuTect2 running, on 5 samples. Three have finished and there is a .vcf and corresponding .idx file for each, each pair with the same time stamp. The other 2 samples have...
View ArticlePresentation slides and tutorial materials - Basel 2016
The presentation slide decks and hands-on tutorial materials can be downloaded at this Google Drive link.
View Articlewrong genotypes are not being corrected through genotype refinement
Hi, I am calling variants in a family and I have observed that some variants are being called homozygous although they are heterozygous because the second allele is present only in a very small amount...
View ArticleGATK 3.0 HaplotypeCaller RUNTIME ERROR
Hi, I am running Haplotypecaller for ~600 bams to perform gVCF call on a cluster (SGE qsub system). Each node has 32 cores, 256 GB RAM. I am running 8 tasks pernode, so each task has 4 cores and 32GB...
View ArticleWhat are the platform requirements and software dependencies for running...
Basic platform Oncotator is written in Python. It can be run on all major Unix-based operating systems (Linux, MacOSX, etc.) that support Python. Unfortunately, running on Windows is not currently...
View ArticleRecalibration plots Error
ERROR MESSAGE: Unable to execute RScript command: Please add the Rscript directory to your environment ${PATH}
View ArticleCode exception in GenotypeGVCFs
Hi all, I meet some error while generate vcf files with GenotypeGVCFs, please help~~ Thanks a lot! my CMD: java -Xmx60g -jar GenomeAnalysisTK-nightly-2016-09-23-gfade77f/GenomeAnalysisTK.jar -T...
View ArticleHaplotypeCaller -ploidy argument
Dear GATK Experts, I have successfully used HaplotypeCaller to call SNPs and generate gVCF files on a number of diploid samples without using '-ploidy' argument. However, when I set '-ploidy' argument...
View ArticleContEst without normal.bam
Hello. We only have tumor samples and don't have the paired normal samples. Can we use panel_of_normal.vcf file that mutect2 generated for over 100 normal samples as the genotypes? I tried the...
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