What types of variants can GATK tools detect / handle?
The answer depends on what tool we're talking about, and whether we're considering variant discovery or variant manipulation. Variant manipulation GATK variant manipulation tools are able to recognize...
View ArticleRegarding ploidy in Haplotyple Caller for multiple replicates of pooled RNAseq
Hi, I am a little confused about the best practices for running Haplotyple Caller to call variants given the pooled nature of my study, any feedback is super appreciated! I have 10 replicates of...
View ArticleVariantFiltration is not filtering?
Hi, I'm trying to filter out variants in a .vcf file that I generated from DNAseq data (BWA->picard->GATK). I'm following the most recent documentation I can find on VariantFiltration and the...
View ArticleI have been trying to run the following command for Queue.jar. But its not...
Command: java -jar Queue-3.4-46/Queue.jar -S call_hs_snps.scala -R human_g1k_v37_decoy.fasta -D dbsnp_138.b37.vcf -H hapmap_3.3.b37.vcf -O 1000G_omni2.5.b37.vcf -T...
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 Article-maxAltAlleles argument ignored in HC and genotypeGVCFs in GATK-3.7?
Hi there I have a similiar issue as described here: http://gatkforums.broadinstitute.org/gatk/discussion/5111/haplotypecaller-pooled-sequence-problem I am using GATK version 3.7-0-gcfedb67 on poolseq...
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Spanning or overlapping deletions (* allele)
We use the term spanning deletion or overlapping deletion to refer to a deletion that spans a position of interest. The presence of a spanning deletion affects how we can represent genotypes at any...
View ArticleCan the results of UnifiedGenotyper and HaplotypeCaller be significantly...
Hi! I'm trying to replicate the variant calling procedure done by a previous graduate student in my lab. To be precise, I have access to the original fastq files and his final vcf file; unfortunately,...
View ArticleERROR MESSAGE: java.lang.reflect.InvocationTargetException in the...
Hi guys I'm having this error (attached) when running SelectVariant on my vcf. I tried deleting the .idx of my vcf (solution recommended) and rerun it but it didn't work. I appreciate any help you can...
View ArticleSpanning deletion in pooled sequencing studies
Hey GATK team, I have a question regarding spanning deletions in one of my runs. Briefly, the study is set up so that we sequenced 21 pools of 3-5 animals each. Using GATK 3.5, I followed the Best...
View ArticleThe contig order in knownSites and reference is not the same
Hi, I tried to use baserecalibrator. Here are my inputs: Human reference: HG38 downloaded from GATK bundle dbsnp_vcf: hg38.dbsnp.vcf (fileformat=VCFv4.2) downloaded from GATK bundle, sorted by Picard...
View ArticleOncotator Error -- Please help me
I am running Oncotator 1.8.0.0 on MuTect2 output .vcf file. I did perform filtering for PASS before running Oncotator. If I run this on command line: oncotator -v --input_format=VCF --output_format=VCF...
View ArticleLimit core usage with CombineGVCF
Hi, I'm trying to merge gvcf files created by the HaplotypeCaller, but I'm seeing some excessive core usage. The options for CombineGVCF do not include --nt, so there's no way I'm seeing to limit core...
View ArticleCross comparison between Array and NGS data
Dear GATK staff, I have a 11 samples that were sequenced using NGS (Illumina HiSeq) and 2 of these samples were also genotyped using an Illumina Human Global screening array (Illumina Iscan). I was...
View ArticleSelectVariants Large VCF slow runtime
I am attempting to subset and filter a large (10k exome sample, 250GB) VCF file using SelectVariants. My goal is to subset by individual samples (iterating over each sample using a custom script and...
View ArticleSelectVariants modifies VCF entries, keeping only the base calls intact.
I am using GATKv3.5. I used SelectVariants as shown below to remove 11 samples from a vcf file: java -jar GenomeAnalysisTK.jar -T SelectVariants -R reference.fasta -V all_samples.vcf -xl_sn sample90...
View ArticleMerging two different data (missing or ref/ref)
Hello, I have two different types of data (one is WES data for 100 cases and another is WGS data for 200 controls). I combined the data respectively (into one WES.vcf and one WGS.vcf) using...
View ArticlePicard LiftOverVcf produces duplicate positions
Hi, I have produced a set of VCF files with UnifiedGenotyper, using a custom BED file. Subsequently I have used Picard LiftOverVcf in order to lift these VCF files from hg38 to hg19....
View ArticlePicard ValidateSamFile failing with INVALID_TAG_NM on hg38 HLA contigs
Picard ValidateSamFile is failing with INVALID_TAG_NM on hg38 HLA contigs when MODE=VERBOSE. The first 100 HLA reads in my BAM file failed. I assume all would fail as there were a number of different...
View ArticlePhasing SNPs and Indels
Hi I was looking into tools for phasing indels and SNPs. It seems that ReadBackPhasing only supports phasing of SNPs. I'm working on data from TCGA, and according to your docs HaplotypeCaller which can...
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