Presentation slides and tutorial materials - Basel 2016
The presentation slide decks and hands-on tutorial materials can be downloaded at this Google Drive link.
View Articleg.vcf masks variants with conflicted reads
I'm working on Salmonella, and one of the major sources of noise in our analysis is that there are some regions of the genome where we have many reads that disagree with the eventual call at that...
View ArticleOut of space when running SplitNCigarReads
I know this question has been asked before. I have read the answers of previous post and did fix by the instructions, but this problem keeping occur. I have checked my storage space, there is enough...
View ArticleInput files known and reference have incompatible contigs.
I am getting the following error from RealignerTargetCreator in GATK 3.6: ##### ERROR MESSAGE: Input files known and reference have incompatible contigs. Please see...
View ArticleVQSR training set
Hi all, I would like to try applying VQSR to my WGS data. What I could use is a SNP database built with GBS on different samples than the ones present in my actual callset. I have a question: do we...
View ArticleReorder Sam error "New reference sequence does not contain a matching contig...
Hi I'm trying to re align bam file using GATK tools. My bam file is currently in lexographical format and I need to convert it karyotipic form. The bam files' chromosomes are numbered as "chr1 chr2..."...
View ArticleWhy does GATK LeftAlignAndTrimVariants set a missing genotype to 0/0?
Hi. I appreciate many your helps. I have one vcf file (a.vcf). This file has one variant data. The data also has missing genotypes "./." because of DP=0. The variant is tri-allelic variant as below....
View ArticleErrors at the end of the SNP calling
Hi I am following the next steps to call variants in RNA-seq data: https://software.broadinstitute.org/gatk/guide/article?id=3891 I am runnig the step 6 of variant calling using this command line: java...
View Articledepthofcoverage: How does depthofcoverage treat reads with SAM flag value 0?
I am getting a discrepancy when comparing gatk depthofcoverage with bedtools coverage -d option. The reads are single and mapped with ion torrent TMAP (5.0.13).
View ArticleFastaAlternateReferenceMaker -- how does it deal with the '*' deletions.
Hi GATK best team, I am having a question concerning FastaAlternateReferenceMaker once again. I was wondering in a case when there is an alternate 0/2 and that the options are A T,* what does the...
View Article(howto) Test your GATK installation
Objective Test that the GATK is correctly installed, and that the supporting tools like Java are in your path. Prerequisites Basic familiarity with the command-line environment Understand what is a...
View ArticleHaplotype caller AF - How to obtain the real AFSpectrum.
Hi GATK team, I just figure out recently that the vcf I produced with HC was producing theoretical allele frequencies. But I would like to have an allele frequency per population (I can always...
View ArticleLocal Realignment around Indels
For a discussion of the implications of removing indel realignment from workflows, see Blog#7847 from June 2016. Realigner Target Creator For a complete, detailed argument reference, refer to the GATK...
View ArticleWorking around Missing AD/DP's from HC output
It is a currently known issue that HC doesn't emit DP/AD at all sites. I wonder how can I filter out those sites using JEXL statements? I know there're statements in bcftools that would do it (...
View ArticleStar allele and weird genotype calling
Dear GATK team, I have an example of a deletion spanning another mutation resulting in a star allele and I need some help to understand the called genotypes. I have 3 individuals. Individual 1 has only...
View ArticleUsing JEXL to apply hard filters or select variants based on annotation values
1. JEXL in a nutshell JEXL stands for Java EXpression Language. It's not a part of the GATK as such; it's a software library that can be used by Java-based programs like the GATK. It can be used for...
View ArticleHow does Picard's MarkDuplicates handle unique molecular barcodes and PCR error?
Hello, I'm interested in using unique molecular barcodes to help distinguish what is PCR error in my samples. My current understanding of how MarkDuplicates chooses a "best-pair" is that it chooses...
View ArticleReduced Representation
Is it possible to use Genome Strip (preprocess, discovery, genotyper) on reduced representation data? In this case, genomic DNA was restricted with PacI, a rare cutter, and for each of 16 samples, the...
View ArticleRealignerTargetCreator problem with vcf file
Hi all! I have a problem with this tool of GATK: RealignerTargetCreator. At the beginning I found this error: FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file...
View ArticleMuTect 2 Output lacking of AD information for Tumor sample
Greetings: I have been working on a WES data, and managed to finished my first round of MuTect2. (Though I used the option -nct 4, it still tack almost 10 days for MuTect2 to finish the analyze.) Below...
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