GATK v3.7.0 SelectVariants discards variant
Hi I've found an usual case where a variant disappears during the hard-filtering workflow. #Joint genotyping /share/apps/jre-distros/jre1.8.0_101/bin/java -Djava.io.tmpdir=/state/partition1/tmpdir...
View ArticleCan missing field values in VariantAnnotator be changed from "0" to "."?
I am trying to use VariantAnnotator on my data. In a few cases, I am passing multiple alleles and my annotation file contains only one of those alleles. For the alleles missing in the annotations file,...
View Article500 reads supporting reference allele, 0 reads supporting the alternate...
For one of my samples at one particular SNP, there appears to 500 reads supporting the reference allele and 0 reads supporting the alternate allele. However, GATK still did not call a genotype:...
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Genotype Refinement workflow
Overview This document describes the purpose and general principles of the Genotype Refinement workflow. For the mathematical details of the methods involved, please see the Genotype Refinement math...
View ArticleGATK (v 3.5) VariantAnnotator ERROR: potential bug?
Hi, I am using VariantAnnotator and, among other annotations, I would like to add also the allelic frequency of my SNPs in 1000G to the resulting annotated .vcf file. I did this through the following...
View ArticleGenotypeSummaries
Hi GATK team, I have a multi-sample vcf file of WES patient samples created by HaplotypeCaller. After applying VQSR, and DP filter, I have got TiTv ratio of 2.59, which is a bit low and should be near...
View ArticleVersion highlights for GATK version 3.7
Here it is at last… as in, last release for 2016, and possibly the last point release of GATK 3 ever! Aside from the usual pile of bug fixes, the new features in this version are actually (almost) all...
View ArticleGATK for Nanopore data
Hi, I'm trying to use GATK to perform variant calling analysis with Minion Nanopore data. In details, I would like to ask you if someone has already used GATK to analyse Nanopore sequencing data, and...
View ArticleHaplotypeCaller generates diff results on different CPUs
I encountered an interesting problem: running HaplotypeCaller on different machines generates different result for 2 sites. The machines use the same input BAM file, same reference, same java...
View ArticlemaxNumHaplotypesInPopulation
Hello! I am reading through the document for "HC step 2: Local re-assembly and haplotype determination" and have a question on the "maxNumHaplotypesInPopulation". For a given region, should the number...
View ArticleMutect build Failure
Hi, I am currently trying to build MuTect on my Linux machine. I have followed the instructions as on the page https://github.com/broadinstitute/mutect/blob/master/README.md. However when I carry out...
View Articlepicard SortSam | picard SetNmMdAndUqTags fails on post reference genome...
I am trying to run a https://github.com/broadinstitute/wdl/tree/develop/scripts/broad_pipelines style pipeline. The picard SortSam | picard SetNmMdAndUqTags fails because BWA aligned some part of the...
View Articleconfusing error message ; complaint of missing header columns that aren't...
Hi, I pass to PadTargets an interval_list file, and it complains of missing columns....but the values are on the first line. Do you by chance notice anything wrong with what I'm doing? Note the...
View ArticleInstalling GATK through cygwin
Hi ya'll I don't have access to the specific instructions for installing GATK on a windows platform (i.e. using cygwin). If I could get permission or someone could walk me through this I would be...
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(How to) Call somatic copy number variants using GATK4 CNV
Presented tools are in BETA. Document is in BETA. It may be incomplete and/or inaccurate. Post suggestions to the Comments section and be sure to read about updates also within the Comments section....
View ArticleNGS mapping for pseudogenes
Hi, We are doing whole exome data analysis using GATK best practices guidelines. There are few genes which has pseudogenes, the mapping quality becomes zero. Such as SMN1 and SMN2, GBA and GBAP1 etc....
View ArticleToo few indels for VQSR in Joint analysis of 75 exomes
Hi, I am trying to execute the pipeline for joint analysis of 75 exomes. I guess it is a reasonable number to use for VQSR but I have the well known problem with the too few INDELs. After the...
View ArticleBuilding MuTect 1.1.7?
I tried to build the latest MuTect according to the readme available at https://github.com/broadinstitute/mutect and I ran into an error. Specifically, there is an error building gatk-protected only if...
View ArticleError I meet when install MuTect on a linux server
Hi, I am trying to install MuTect on a linux server. By the instruction, I did the steps: make a new source directory (e.g. mutect-src) mkdir mutect-src cd mutect-src get MuTect source git clone...
View ArticleMixed sites annotated with InbreedingCoeff=NaN (GATK GenotypeGVCFs v3.7.0)
Hi I've noticed MIXED sites emitted by GATK GenotypeGVCFs v3.7.0 contain InbreedingCoeff not a number. Is that expected behaviour? Example: 1 116268178 . GAAAA G,GA,GAA 23016.74 ....
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