Questions about GenotypeVCFs output
Hi, I generated 12 .g.vcf files with HaplotypeCaller in GVCF mode and then a vcf with GenotypeGVCFs. What's the easiest way to split this vcf per sample ? Should I apply hard filtering first and then...
View ArticleVariantFiltration | HaplotypeCaller - ignoring variants close (5bp) from...
Hi, I am currently working with data from HaloPlex Target Enrichment System. HaloPlex is using retriction enzymes to digest the DNA, thus producing non-random reads and often have false mutations in...
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ERROR MESSAGE: Illegal base [ ] seen in the allele when running...
Hello everyone, It's me again Since I have finally worked through where to apply the parametre -trimAlternates, now I got another question. When I running FastaAlternateReferenceMaker, I got the error...
View ArticleVariantAnnotator using GnomAD gives NullPointerException
Hello, Running VariantAnnotator, I am running into errors I couldn't find solutions for in the forum. Using the GnomAD publicly available VCF's, I would like to add information to a VCF, specifically...
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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 ArticleAre there any plans to add multi-interval support to GenomicsDBImport?
The reason I ask is that it's rather annoying when you've chunking your input data and one of your chunks crosses a chromosome boundary. it seems like according to the Github docs thqt GenomicsDB...
View ArticleDifferences between GATK 4.beta.5 vs 4.0.0.0 HaplotypeCaller results
Hi! I'd like to perform short germline variant calling on human DNA-seq samples (separate analysis of WES cohort and PCR-free WGS cohort, both paired end). The plan is to follow GATK best practices of...
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Base Quality Score Recalibration (BQSR)
BQSR stands for Base Quality Score Recalibration. In a nutshell, it is a data pre-processing step that detects systematic errors made by the sequencing machine when it estimates the accuracy of each...
View ArticlePicard LiftoverVcf: contig not part of the target reference
Dear GATK team, I am trying to liftover a vcf file from hg19 to hg38, by running the command java -jar ~/tools/picard-2.1.0/dist/picard.jar LiftoverVcf I=input.chr22.vcf O=hg38.chr22.vcf...
View ArticlelibVectorLoglessPairHMM is not present in GATK 3.8 - HaplotypeCaller is...
We are running GATK on a multi-core Intel Xeon that does not have AVX. We have just upgraded from running 3.4-46 to running 3.8, and HaplotypeCaller runs much more slowly. I noticed that our logs used...
View ArticleMuTect2 and smalls mpileup reads info seem to be very different?
Hi - I used MuTect2 to call variants in multiple samples from one patient. However, I wanted read information for those samples where a mutation wasn't detected in all the samples and decided to use...
View ArticleA logical problem with SplitCommonSuffices and MergeCommonSuffices
@Sheila @valentin @depristo For example ： A+x -> y (A+x,y is a point) B+x -> y after SplitCommonSuffices A -> x -> y (A,B,x,y is a point) B -> x -> y after MergeCommonSuffices A ->...
View ArticleError while running BaseRecalibrator
Hello, I was running the BQSR on the RNAseq reads. This is the command i typed: java -jar /usr/local/bin/GenomeAnalysisTK.jar -T BaseRecalibrator -R ../../../genome/hg38/hg38.fa -I a_split.bam -L 22...
View ArticleCan GATK4 be used in old shell scripts as GATK3 (without WDL)?
Can GATK4 be used in old shell scripts as GATK3* (and is there a point of changing) without planning to use wdl? Is GATK4 faster (if it can be used locally as GATK3)
View Articledefine java to use in GATK4?
Hi, today I tried to run GATK4. But I ran into an issue. Just calling "gatk" looks fine, but when running "gatk --list" produces the following output. Running: java...
View ArticleMuTect- small fraction of tumor contamination in normal samples.
Hi, We have normal samples that have a small fraction of tumor contamination. usually less than 10%. Is there a modification we can apply to mutect that can maximize the sensitivity and specificity of...
View ArticleMutect 2 B38 germline resource
Hi, Congratulations on GATK 4.0! I'm looking at the instructions for Mutect2 where it suggests using a germline resource "--germline-resource af-only-gnomad.vcf.gz". Do you have a version of this for...
View ArticlePanel of Normals (PON)
A Panel of Normal or PON is a type of resource used in somatic variant analysis. Depending on the type of variant you're looking for, the PON will be generated differently. What all PONs have in common...
View ArticleUsing GenomicsDBImport to consolidate GVCFs for input to GenotypeGVCFs in GATK4
In GATK4, the GenotypeGVCFs tool can only take a single input, so if you have GVCFs from multiple samples (which is usually the case) you will need to combine them before feeding them to GenotypeGVCFs....
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PGT and PID is a dot
Hi, I am following the best practice pipeline with version 3.6 of gatk and in order to reduce the amount of compound heteozygote variants found in my analysis, I recently chose to "mature" into using...
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