How about VQSR variant set if the reference not the hg38
Hi, There is a question when I run GATK. My goal is get variant from multiple sample in the rice. And I get a raw variant from HaplotypeCaller, and followed CombineGVCFs, GenotypeGVCFs according to the...
View ArticleInput file for intervals argument
Hi All, I am currently running MuTect 2 on my files. However, this is taking quite a deal of time per tumour/ normal pair analysis. I have read that using the intervals argument would decrease runtime....
View ArticleVQSR filtering options for hg38
The examples you shown here for the VQSR filtering (SNP and INDEL) model https://software.broadinstitute.org/gatk/guide/article?id=1259. Are they specific to a reference genome say hg37? What suggested...
View ArticleI am unable to use VQSR (recalibration) to filter variants
The problem: Our preferred method for filtering variants after the calling step is to use VQSR, a.k.a. recalibration. However, it requires well-curated training/truth resources, which are typically not...
View ArticleHow could I make only one VCF out of the four?
I have created 4 Exome VCF from four members family. How could I make only one VCF out of the four? Thanks!
View ArticleHow does MuTect2 assign germline_risk filter
I have read MuTect1 paper and MuTect2 code, and it seems the germline risk is assigned this way 1. if variants in dbsnp, but not cosmic, the nlod cutoff is 5.5 2. otherwise, the cutoff is 2.2 Some of...
View ArticleHaplotype caller in GATK 4, a.k.a the hellbender
I am trying to use GATK 4 to run the tools in a scater/gather fashion using Spark. For example, I was able to run printreads using PrintReadsSpark. However, now I am trying to run the Haplotype caller,...
View ArticleAllele Depth (AD) is lower than expected
The problem: You're trying to evaluate the support for a particular call, but the numbers in the DP (total depth) and AD (allele depth) fields aren't making any sense. For example, the sum of all the...
View ArticleBase Quality Recalibration With Low Frequency Variants
Hi I'm working on calling low frequency heteroplasmic variants in the mitochondrial genome, using WGS data. My data is high coverage (~2000x), and heteroplasmic variants might be represented on as few...
View ArticleI need help. GATK Haplotypecaller says my dict is empty but it isn't??
The Error message I get is the following INFO 12:25:14,659 HelpFormatter - ---------------------------------------------------------------------------------- INFO 12:25:14,662 HelpFormatter - The...
View ArticleMutSigCV Coverage File
In the sample file for MutSigCV gene coverage file, for each mutation, there is coverage for each sample. Is this coverage the alternative coverage on tumor sample? But if I try to get the information...
View ArticleCombineVariants resets AF to 0.5 and 1.0
Dear GATK Team, I have been using CombineVariants to merge SNPs.vcf and Indels.vcf of the same sample into a single vcf file. In the SNP.vcf and Indels.vcf files, I have changed the value for AF tag in...
View ArticleIncorrect Likelihood / AD Count For Variant
I am trying to figure out why a site is being called with the wrong AD / Likelihood and what can be done about it. In particular, there is a site in my VCF that is being called with a very wonky AD...
View ArticlePreserve Case when Using FastaAlternateReferenceMaker
I had soft masked a FASTA file using BEDTools' maskfasta and wanted to use this as input to FastaAlternateReferenceMaker as well as a VCF file. I was suprised to see that FastaAlternateReferenceMaker...
View Article1000Genomes vcf file and correct reference genome used in...
I am using a vcf file from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ Specifically, chromosome 20. 1000Genomes says their reference genome is GRCh37, which is the same as hg19. However,...
View Articleinvite GATK group for a workshop
Hello! We are non-profit organisation. And we plan to invite GATK team for a on-site workshop in the fall of 2017. Could you please tell me whom should we contact with for this? thanks! Ying
View ArticleHaplotype caller-generated VCF cannot be validated
Hi, I have VCFs generated by Haplotype Caller and Unified Genotyper on the NA12878 genome. Running Variant Recalibrator brings up errors in the VCF, so I'm attempting to understand them using GATK...
View ArticleMax Alt Alleles behavior
I'm using HaplotypeCaller to call a vcf file with 8 samples. I left the --max_Alt_Alleles argument at its default 6. However I'm getting some odd warning messages: WARN 19:12:58,670 ExactAFCalc - this...
View ArticleHow do I turn off INDEL calling in HaplotypeCaller (i.e. only call SNPs)?
I know that for UnifiedGenotyper the option is -glm, but I don't see that available for HaplotypeCaller.
View ArticleWhy does GATK LeftAlignAndTrimVariants set a missing genotype to 0/0?
Hi. I appreciate many your helps. I have one vcf file (a.vcf). This file has one variant data. The data also has missing genotypes "./." because of DP=0. The variant is tri-allelic variant as below....
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