ERROR running SplitNCigarReads on RNAseq data using Ensembl Mus Musculus...
I was trying to run this commands ~/downloads/gatk-3.7 -T SplitNCigarReads -R ~/refFiles/Mus_musculus/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa -I...
View ArticleCustom Walker :
Hi all, I'm playing with the GATK3.6 API, writing a custom walker. @DocumentedGATKFeature( summary="Annotate Variants with eigen data", groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs =...
View ArticleGATK 3.6 api: GATK cannot find my Walker when I use a java lambda / Filter ?
Hi all, I'ts cross-posted on SO: http://stackoverflow.com/questions/41678374 I've written a custom plugin for GATK 3.6 $ javac -version javac 1.8.0_60 My walker was compiled but wasn't found/loaded by...
View ArticleAnnotation is lost when merging GVCF files with GenotypeGVCFs
Dear GATK team, The StrandBiasBySample annotation works fine with the HaplotypeCaller but then when I merge all my GVCF files into one with the GenotypeGVCFs tool I loose this information for all my...
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(How to) Map and clean up short read sequence data efficiently
If you are interested in emulating the methods used by the Broad Genomics Platform to pre-process your short read sequencing data, you have landed on the right page. The parsimonious operating...
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(How to) Generate an unmapped BAM from FASTQ or aligned BAM
Here we outline how to generate an unmapped BAM (uBAM) from either a FASTQ or aligned BAM file. We use Picard's FastqToSam to convert a FASTQ (Option A) or Picard's RevertSam to convert an aligned BAM...
View ArticleCombineVariants --variants : can I give both a variant name and a file type?
I am trying to run tool CombineVariants on 3 vcf files. There is an extra dot in the file names which I expect is why dynamic determination of type is not working. I want to rename the variants, not...
View ArticleHow can I prevent the file header from showing up in gigantic font?
Hi. My question is, when I post to the forum, some parts of my post become huge, e.g. file headers or error messages. I'm showing a truncated example below of a VCF header. How can I prevent this from...
View Article(howto) Call variants with HaplotypeCaller
Objective Call variants on a single genome with the HaplotypeCaller, producing a raw (unfiltered) VCF. Caveat This is meant only for single-sample analysis. To analyze multiple samples, see the Best...
View ArticleGATK CNV Toolchain in Firehose and FAQ (Broad Internal)
We have put the GATK4 Somatic CNV Toolchain into Firehose. Please copy the below workflows from Algorithm_Commons GATK_Somatic_CNV_Toolchain_Capture GATK_Somatic_CNV_Toolchain_WGS For questions and...
View ArticleGradle test failed after building GATK 4 Alpha
Hi, I've just downloaded GATK 4 (from https://github.com/broadinstitute/gatk/) and successfully built it with ./gradle installAll command. But after I run the ./gradle test command, it only completed...
View ArticleHaplotypeCaller pooled sequence problem
Hi, I have a number of samples that consist of multiple individuals from the same population pooled together, and have been truing to use HaplotypeCaller to call the variants. I have set the (ploidy to...
View ArticleGATK HaplotypeCallerQUAL field changes while running per chromosome
Dear GATK Team, I ran GATK haplotypecaller (3.4) on one sample. In normal procedure . Whole bam file submitted to haplotype caller. 2 .In another way, BAM was splitted by chromosome ( using -L option)...
View Articleerror CombineVariants UNIQUIFY
Hello, I am trying to merge 2 vcf for same sample with 2 different caller (like GATK UG and HC) I use CombineVariants tools with -genotypeMergeOptions UNIQUIFY option. comande line : java -jar...
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(How to) Map reads to a reference with alternate contigs like GRCh38
Document is in BETA. It may be incomplete and/or inaccurate. Post suggestions to the Comments section and be sure to read about updates also within the Comments section. This exploratory tutorial...
View ArticleMissing positions after GenotypeGVCFs
Hi, Sorry if this is a re-post but I have read through the last post on this issue: http://gatkforums.broadinstitute.org/gatk/discussion/4343/missing-positions-in-the-gvcf-file I'm having the same...
View ArticleIndelRealigner
Hi. I am doing a matched Normal-Tumor mutation detection with whole exome sequencing data. When evaluating my pipelines, I noticed that some somatic mutations are not showing if I follow the best...
View ArticleMutect 2 for amplicon sequencing
Hello I am trying to use Mutect2 to call variants using a PON and no germline sample and had a few questions about my results. I am using the illumina myeloid amplicon panel for library prep. All the...
View ArticleCatVariants Error - Features added out of order
I am running the practices pipeline on a large set of WGS data. On some of the CatVariants steps I am getting errors with the GATK v3.5. there are errors:
View ArticleMutect2 ERROR: Null qss lines in bcbio log
Hi, I'm running bcbio mutect2 tumor/normal somatic variant calling on a linux cluster environment. I had to restart my job owing to an error in the bcbio config file (*.yaml), and upon editing the...
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