MuTect2 all potential somatic mutations did not pass the alt_allele_in_normal...
Hello, I am trying to use MuTect2 to call low-frequency (0.1-5%) mutations in yeast population but none of them passed the alt_allele_in_normal filter, meaning the allele is presented in control...
View ArticleGATK3 HC bug?
Hey GATK Devs! I'm writing to report some unexpected behavior on the part of GATK3.8 HC. I'm trying to use Illumina data to call SNPs and indels on a PacBio assembly and identify loci where assembly...
View ArticleGATK events update for Fall 2017: ASHG and more!
Fall is my favorite season -- it combines the best weather in New England and the most active period of the year for GATK events and announcements (although sometimes the latter means we don't get to...
View ArticlePicard LiftoverVcf
I am having a problem with picard's LiftoverVcf. I am trying to Liftover hapmap files (downloaded plink files from hapmap and converted to vcf using plink) from ncbi36 to hg38. I was able to do this...
View ArticleMost Variants Called
Hello all! So I am forced to do hard-filtering on my VCF files. Looking at them before filtering, ~99% of my variants have a QD of <2.0. Looking at the distribution plots in ggplot, they do not...
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How to produce GVCF files that were produced from a different reference genome?
Hi everyone. I have got my genotyped vcf file successful produced but I needed to merge them with other g.vcf files I recently received from a collaborating company. These were gzipped vcf files with...
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Difference between vcf-result and "samtools tview"
I am calling mutation contained in the genes brca1/brca2 with haplotypecaller. I use "samtools tview" to check if the result is right. Cite a deletion site as the example,I got the result as the...
View ArticleGATK 3.5 FindCoveredIntervals works same regardless of DuplicateFilter tag
Hi, When using FindCoveredIntervals tool, I find no difference when calling the tool with -drf DuplicateRead tag, or without it (when using -rf DuplicateRead tag). Manual checking of .bam file using...
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(How to) Call somatic copy number variants using GATK4 CNV
This demonstrative tutorial provides instructions and example data to detect somatic copy number variation (CNV) using a panel of normals (PoN). The workflow is optimized for Illumina short-read whole...
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 ArticleRead groups
There is no formal definition of what is a read group, but in practice, this term refers to a set of reads that were generated from a single run of a sequencing instrument. In the simple case where a...
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Understanding and adapting the generic hard-filtering recommendations
This document aims to provide insight into the logic of the generic hard-filtering recommendations that we provide as a substitute for VQSR. Hopefully it will also serve as a guide for adapting these...
View ArticleGATK 4.0 will be released Jan 9, 2018
A long time ago in a galaxy far, far away, we started work on a brand new version of GATK in which the engine framework was to be completely revamped, streamlined and accelerated, with support for...
View ArticleHow does GATK4 Mutect2 know which -I is tumor?
Hi, I'm reading the Mutect2 documentation here: https://software.broadinstitute.org/gatk/gatkdocs/4.beta.1/org_broadinstitute_hellbender_tools_walkers_mutect_Mutect2.php I see that you give two -I...
View ArticleOncotator error---IndexError: list index out of range
I used Oncotator (1.9.3.0) to annotate VCF file. If I run this on command line: oncotator -v --input_format VCF --output_format TCGAMAF --db-dir /share/apps/oncotator_v1_ds_April052016/ -d ....
View Articleabout genotypegvcfs
I want to know about the algorithm which converts raw gVCF files from different samples to raw VCF by doing genotypegvcfs
View Articlefinal result
The question is that after running GenotypeGVCF, and getting VCF file then how we can get the result for every sample we have run GenotypeGVCF. I mean if we run haplotyping for 100 samples and getting...
View ArticleInstall GATK 1.0
We need to re-analyze some data produced some years ago and I need to install the first GATK version on my local machine. From the following link https://github.com/broadgsa/gatk/releases?after=1.5 I...
View ArticleGATK Community - Take this survey, win a prize!
As many of you know, GATK4 Beta is out and we are excited for the full GATK4 to be released in the new year. It has been a long time coming and we hope that many of you have gotten to experiment with...
View ArticleWhen will GATK4 release to general availability status?
We've already used GATK4 beta 5 for testing,and want to know when will GATK4 release to general availability status?THX.
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