Failings in BadCigarFilter, BadMateFilter, and others
Hi, everyone, I'm using GATK tools to perform local realignment around indels. For that, I run first: java -jar $GATK -T RealignerTargetCreator -R dmel_ref.fasta -I "$i.rmdup.srt.bam" -o...
View ArticleHow do SelectVariants and VariantEval handle spanning deletion "*"?
Hi, I have recently used GATK 3.5 to run joint calling (GenotypeGVCFs). After that, I used SelectVariants to select one sample and ran VariantEval with the sample's data. However, I am curious about...
View Articlesome questions about difference between HaplotypeCaller and MuTect2
Hi, Recently I have been worked in variant calling using GATK and I have some questions in the process of learning GATK tools. I’m interested in the essential difference between HaplotyepCaller and...
View Articlefiltering by mapping quality
I've been following GATK Best Practices for WGS/WES. It's very comprehensive. One thing that's missing is any mention of mapping quality filtering. A lot of tools are already using MappingQualityFilter...
View ArticleQuestion about unknown in oncotator results
Dear Oncotator developers, I am trying to use Oncotator to annotate MAF or VCF files. According to instruction in this forum, I tried to run with test data "Patient0.snp.maf.txt", then Oncotator...
View ArticleOncotator: Variant Type SNP/Type of Mutation
I am working on a project with several point mutations. I used oncotator to verify the type of mutation (ie. missense, nonsense, etc) and to see if they were unique mutations or SNPs. I received a...
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Upcoming GATK workshop: September 26-28 in Basel, Switzerland
Believe it or not we've done seven workshops so far this year, spread across five countries, spanning three continents -- the furthest ones in Australia (Sydney and Melbourne) and the most recent one...
View ArticleSelectVariants
I am trying to select heterozygotes from the VCF file. I use this command many times and it works all the time. But something error pops up this time, do not know what is the problem. I check the...
View ArticleGATK Runtime error
Dear GATK team, While running GATK3.6 on DNANexus, I came across an error with stack trace and I'm not sure what the problem is. Below is the message that I got: ERROR stack trace...
View ArticleLong tips in phylogeny after GATK best practices for variant calling
I have a population of 60 relatively closely related samples (non-human). After running through the GATK best practices to identify variants (with hard-filtering instead of VQSR), the phylogenies I...
View ArticleMuTect2 PON CombineVariants
In the MuTect2 documentation, it says: "For full PON creation, call each of your normals separately in artifact detection mode. Then use CombineVariants to output only sites where a variant was seen in...
View ArticleAF calculation in Mutect2
Hi, I've been calling somatic mutations with Mutect2, and have noted that the AF calculation does not always correlate to DP alt/(DP ref+DP alt). For example, consider this indel: T057.mutect2.vcf:7...
View ArticleIs there any way to see all reads after realignment by HaplotypeCaller?
If I have understood correctly, then the bam file produced by -bamout only contains reads which have been realigned? It doesn't include the original reads which haven't been realigned? If this is so,...
View ArticleGATK Runtime Error NullPointerException while running Haplotype Caller
Hello, I am trying to run the HaplotypeCaller and have run into a RunTime Error. I am using GATK version 3.5-0-g36282e4 I am running the command as follows: java -jar...
View ArticleFastaAlternateReferenceMaker leaving out verified SNPs from FASTA file
I have Illlumina sequenced genomes that I have aligned using BWA and GATK to a section of a genome that I am interested in. When I examine the .bam file and the VCF file generated in IGV I can clearly...
View ArticleDepth Coverage
I have calculated the depth coverage using GATK for my bam file and now i would like to plot histogram for the same. Which file and which tool should i use. My genome is in scaffolds and almost 250...
View ArticleCRAM version in GATK 4.0
what version of CRAM will be supported as part of GATK 4.0? Thanks! Severine
View ArticleBug Report: ReadBackedPhasing does not handle reads with mapping quality 255.
A valid SAM record with a 255 mapping quality causes the following error when running ReadBackedPhasing. I am using version 3.6-0-g89b7209. Looking at the source, PhasingRead.java:68 calls...
View ArticleQuestions about filtering variants manually
This discussion was created from comments split from: How can I filter my callset if I cannot use VQSR / recalibrate variants ?.
View Articleoutput.plots.R.pdf is empty
My output.plots.R.pdf is empty. I suppose there is an error in the Rscript. When I rerun the output.plots.R there is the following error. Any idea why that is happening? Warning message: Non Lab...
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