How does phase by transmission deal with X chromosome variants
I have some new vcf files that are phased by transmission. There are numerous calls that change from 1/1 with haplotype caller to 1|0. Can you tell my why this is the case or is it because pbt doesn't...
View ArticleBug when filtering INDELs?
Hi guys I am using GAT3.7, I subsetted my SNPs and Indels, filtered the SNPs and then wanted to run my filters on the Indels but get an error that looks like a bug, here the log file INFO 09:54:57,570...
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Reference Genome Components
Document is in BETA. It may be incomplete and/or inaccurate. Post suggestions to the Comments section. This document defines several components of a reference genome. We use the human GRCh38/hg38...
View ArticleGenotypeGVCFs Runtime
Hello, I'm running GenotypeGVCFs on 60 .g.vcf files. Each .g.vcf.file is about 4G. I had given it about 100G memory and 30 cores. It doesn't seem to like the options options -nt -nct to multi thread....
View ArticleMutation calling rules for targeted sequencing of 4 genes
Dear GATK team, we are validating our findings on a large cohort of 150 patient samples. We are sequencing only 4 genes using Fluidigm amplicons on MiSeq system. Since there are only 4 genes and some...
View ArticleBuilding GATK 3.7 and a stackoverflow building Queue Extensions
Occasionally when my CI docker image build runs mvn verify, it gets a stack-overflow error when building GATK Queue Extensions Distribution. This is not 100% of the time and hard to reproduce...sorry...
View ArticleCan't post a discussion on the forum
I've beed trying to post a question and it gets rejected every time. There is nothing special with this question except for the fact that I have a couple of link. When I click on the post discussion...
View Articleregion with GQ=0 in GVCF despite high read depth
Dear, We have aligned RADseq data to a reference genome and created multiple individual GVCF files. One particular subregion of approx. 10bp, with good read depth (~50-200), shows a Genotype Quality...
View ArticleGATK CallSegments
I see CallSegments mentioned in a few tutorials and posts. However, there does not seem to be any documentation for it. Is it possible to get more info? Is that basically the next version of ReCapSeg?
View Articleabout SVAnnotation
Dear all, please could you let me know, are SVToolkit.jar and SVAnnotation tools that are still under active development ? Thank you ! -- bogdan
View ArticleMuTect2 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 Articleremove duplicates by running Picard's MarMarkDuplicates and...
Dear all, I use the following pipeline for removing duplicates from a sorted.bam file: =============MarMarkDuplicates ============== java -jar...
View ArticleQD annotation not found: Variant Recalibrator error
Hi GATK community, While working on the GATK pipeline for variant analysis, we have been getting the same error (below) repeatedly, in several scenarios we had tried prior to posting here.This is the...
View ArticleInterpreting ExcessHet INFO field
Hi team, First thanks for the wonderful help and clarity of explanations on this website. I am considering applying a filter on ExcessHet on my vcf files to have only markers that follow HWE. I...
View Articletoo many memory and file handle resource required by GenotypeGVCFs
Hi. It seems that too many memory and file handle resource required by GenotypeGVCFs command line: java -XX:-UseCompressedOops -Xms1440g -XX:MinHeapFreeRatio=25 -XX:MaxHeapFreeRatio=50 -jar...
View ArticleGQ
Hi, I found some strange rules from my VCF file. Most of snps which had high GQ, they also had high AF. However, why the snp which had low AF,they got low GQ? Does it make sense? Thanks for your help....
View ArticleMutect2 without all normals
Hi, I have cancer samples for a set of 44 patients among which I have 11 sain controls (so, I have sain controls for 1/4 of my patients). Can I perform Mutect2 to call variants using -artefact_mode for...
View ArticleCombining variants from different files into one
Solutions for combining variant callsets depending on purpose There are three main reasons why you might want to combine variants from different files into one, and the tool to use depends on what you...
View ArticleGenotypeGVCF: skipped sites
Dear devs, I'm working on GATK v.3.7 in order to genotype more than 700 samples. Before using GenotypeGVCFs, I used CombineGVCFs. GenotypeGVCFs works fine, but I'm looking for a solution about this...
View ArticleGATK and MuTect licensing moves to direct-through-Broad model
We have some important news to share with you regarding the licensing of GATK and MuTect. The licensing agreement between us and Appistry will end effective April 15, 2015; from that point on, the...
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