Metadata for Human b37
Hi, Do you have any plan to provide Human b37 reference metadata? Thanks!
View ArticleVariantAnnotator 3.6-g89b7209 writes out a VCF file with BCF or other binary...
Hi, my shell script is looping over several input VCF files from SnpEff-4.1e and adjusts the annotation. java -jar GenomeAnalysisTK.jar -T VariantAnnotator --num_threads 16 -R...
View ArticleReturning different files for each haplotype using FastaAlternateReferenceMaker
Hi, I'm trying to generate FASTA files from a VCF file. My VCF files contain haplotype information (as '0|1', '0|0', and '1|0'). I want different FASTA files for each haplotype, but can only get one...
View ArticleWhat is the cause of this error: ERROR MESSAGE: Invalid argument value...
I have installed GATK2 into a galaxy cloud instance to use the Unified Genotyper for our sequencing course. However, when I run the tool I get the following error message: Dataset 41: Unified Genotyper...
View ArticleDepthOfCoverage rounding up to 100 percent
Dear GATK (aka. Dear Geraldine:)) I've recently experienced that DoC rounds off the "%_bases_above_30" up to 100% in the sample_summary output for one of our gene panels for certain samples, albeit a...
View ArticleHaplotypeCaller Error on some bam files
Hello GATK team, I report an error using HaplotypCaller on 3 bam files (other 34 bam files were processed without problem) Exemple: $ nohup /opt/java/jre1.8.0_102/bin/java -jar...
View ArticleMuTect2 Haplotypes
Hi, I am struggling to figure out, how MuTect2 calculates allele frequencies. Based on a previous problem [1] caused by non-deterministic calls when run on multiple CPU cores, I have decided to run...
View ArticleRead groups names in a BAM file with multiple lanes
Hi, I just downloaded a few BAM files from the GDC data portal. some of them have numerous lines for their read groups information, typically the exome data. when I look for the information with...
View ArticleASEReadCounter
Dear GATK team, I am doing an allele-specific expression analysis using RNA-seq data. I am trying to run ASEReadCounter to calculate read counts per allele and use Mamba (or other downstream tool) for...
View ArticleSplitNCigar with draft assembly?
Hi, I'm trying to use the RNAseq best practices to call SNPs in transcriptomes aligned to a draft assembly for a non-model species. Everything has worked fine so far, but when I try to use SplitNCigar...
View Articlegatk haplotypecaller for gvcf
Hi, I have used gatk HaplotypeCaller to generate a gvcf for a single chromosome. There was an error shown below: Anyone knows what can cause this? For the other chromosomes, it can successfully...
View ArticleRemoval of sites with only '*' mark in ALT field when subsetting samples
Hi GATK team, I noticed an issue, which might be a bug, relating to removal of sites with only '*' mark in ALT field when subsetting samples. Assume we have a deletion, and there is one SNP within this...
View ArticleRecommended protocol for bootstrapping HaplotypeCaller and BaseRecalibrator...
I am identifying new sequence variants/genotypes from RNA-Seq data. The species I am working with is not well studied, and there are no available datasets of reliable SNP and INDEL variants. For...
View ArticleHigher concordance between genotypes representing reference homozygotes than...
Hi, I sequenced two times 66 newt individuals in few hundred loci to a moderate coverage (45 on average). Now I want to check genotype concordance in various depth classes to answer the question which...
View ArticleREF ALT conversion - multiple sample vcf > single sample vcf + trimAlternates
Dear GATK Team, I have extracted the first sample of the following multiple sample vcf example: chr1 3007281 . CCTT CT,C 3654.92 ....
View ArticleCan I apply the germline variant joint calling workflow to my RNAseq data?
We have not yet validated the joint genotyping methods (HaplotypeCaller in -ERC GVCF mode per-sample then GenotypeGVCFs per-cohort) on RNAseq data. Our standard recommendation is to process RNAseq...
View ArticlePanel of Normal and Match-Normal relation
Hello GATK team ! (again) I am now doing my pipeline again with more samples, coming from the GDC data portal. So this time I will have a matched-normal for every samples. I am also considering to...
View ArticleHaplotypeCaller creates an empty VCF file and exits during cmdline args parsing
Hi, it is a bit annoying tha HaplotypeCaller at least exits because of say unsupported combination of commandline switches but provided it has already created a new VCF file for its output, the empty...
View ArticleMuTect2 does not call tumor-only variants
Hi, I'm trying to use MuTect2, however I'm not getting tumor-specific variants called. To get MuTect2 working I'm using an artificial tumor/normal data set, however, somatic mutations I introduced are...
View Articlewhy is 3122x coverage not called 0/0 but ./.
I was running GENOTYPE_GIVEN_ALLELES and found some ./. calls that should be 0/0? For example, this command E:\GamidorFirst\Alignment_1\20161130_152325>java -jar "E:\GenomeAnalysisTK.jar" -T...
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