Ask about chromosomal CNVs of a large number of chromosomes
Hi, I'm using GATK to call CNVs. It works well for the cases of individual chromosomal CNVs as shown in the tutorial materials. But for the following case, which involves chromosomal CNVs of a large...
View ArticlePublication of a Master Thesis that used MuTect2
Hi GATK ! I just finished a Master Thesis which was named: "Detection of Somatic Mutations in RNAseq data from Glioblastoma". The professor was pretty happy with the results that we obtained and wanted...
View ArticleRNASeQC: Any parallelization
Hello, Does anyone know if there is a way to parallelize RNASeQC. From what I can see, it's only using about 1 thread, even when I provide it multiple samples. (I'd like to run it on 96 at once.) If...
View Article(howto) Install and run Oncotator for the first time
1. Download the Oncotator package, the default datasources package, and (recommended) transcript override list from the Downloads page Please note: Broadies who wish to run the installed Oncotator on...
View ArticleAdvice ERROR ----------
I am using the workflow for best practices for variant calling. I used the sam files obtained with bowtie So far I index and create the .dict files using this commands: java -jar...
View ArticleHeterozgyous variants have unbalanced allele depth distribution
Dear all, I was inspecting the frequency of the alternative allele at heterozygous variant sites in 16 exome sequencing samples. In each sample, I selected heterozygous variants with just one...
View ArticleNo 0/0 and I see 0/1, 1/1 and 1/2 GATK SNP call
Hi All, I don't see any "0/0" call, the final "*_final_snp.vcf" file has "0/1, 1/1 and 1/2". I also loaded the two sample I run on IGV and saw a few instances. One sample called 0/1 and the second...
View ArticleSelect SNP and reference monomorphic sites from a large callset
Dear all, Recently, I have called genotype using GenotypeGVCFs with --includeNonVariantSites. I want to pull out the sites with one allele or . in ALT column. I found the following command will also...
View ArticleMutect2 --artifact_detection_mode for tumor-only calling : can i use PoN
I am aware that "Tumor-only variant calling is possible but it is not supported with Mutect2". Thing is, i am working on a study with few normals. I did create my PoN with the 10 available normals. I...
View ArticleMutect2 with lastest nightly build problem
Hi, I am trying to run the variant calling step for the first time as a test. As I don't have any matched normal, I have only my tumour .bam file and a PoN composed of only 2 samples (for now). So I...
View ArticleCombine already merged gVCFs
Hi, We have two NextSeq Runs per week and end up with a gVCF file of around 40Gb per run. A few of those are easy to handle but at some point it will become too much. Not only in terms of disc space...
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 Articlepicard MergeBamAlignment function require paired reads
Does picard MergeBamAlignment function require paired reads as ALIGNED_BAM? This is not mentioned in the picard documents However, we use trimmomatic to do reads QC, which generates three outputs:...
View ArticleSomatic mutations of epithelial cells (HaplotypeCaller vs Mutect)
Hello, I'd like to extract somatic mutations from normal epithelial cells of cancer patients. And it's confusing which tool to use. HaplotypeCaller or Mutect? I know Mutect is for calling somatic...
View ArticleTimeout acquiring a lock - caused by GC pauses
I am trying to run GenotypeGVCFs over a couple of hundred whole genomes. Besides the fact that it uses obscene amounts of RAM, I noticed that it was failing with the message: ERROR MESSAGE: Timeout of...
View ArticleGenerateHaploidCNVGenotypes error
Dear all After running CNVDiscoveryPipeline, I want to get the information of genotype for each sample. But when I running GenerateHaploidCNVGenotypes, an error occurred to me (like following). The...
View Articlejava error in hmm accelerationof HaplotypeCaller, possibly a GATK bug?
Dear GATK team, running the HaplotypeCaller with GATK 3.7, I recently got a reproducable java error which can be circumvented by disabling the pairHMM acceleration of HC by adding the...
View ArticleHaplotypeCaller strategy on a large cohort of Whole Genome samples
We have to perform HaplotypeCaller variant calling on a cohort of Whole Genome Samples (~400 samples). Since the region to be called is huge, I was wondering what would be the best way to go about...
View ArticleError Best Practices links for Exome Germline Variant Calling broken!
robert.stones@newcastle.ac.uk
View Article