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Base Quality Score Recalibration (BQSR)
BQSR stands for Base Quality Score Recalibration. In a nutshell, it is a data pre-processing step that detects systematic errors made by the sequencer when it estimates the quality score of each base...
View ArticleinputFileIndexCache isn't defined error?
I am running the local example test run found in the cookbook. I have downloaded and unpacked all files properly. I have edited the necessary files to call the proper file folders. On each run, the...
View ArticleCromwell/WDL script can't find bwa index
I have a WDL script that is just supposed to do alignment using bwa mem, but I'm getting this error in the stderr log: [E::bwa_idx_load_from_disk] fail to locate the index files My script: workflow...
View ArticleGTF file for b37 from GATK bundle
Hi, There's a lot of posts about this out there but I want to make sure I get the right file. I've downloaded b37 genome from https://software.broadinstitute.org/gatk/download/bundle. I want a GTF file...
View ArticleIs there a place I can find documentation for...
Hello, I was wondering if anyone has an explanation about the metrics produced by UmiAwareMarkDuplicatesWithMateCigar, specifically, the UMI metrics file. I could probably guess for most of them, but...
View ArticleMutect2/GATK4.5 error
Hello, I am generating normal vcf files using tumor-only mode with Mutect2/GATK4.5 and bam file after BQSR. I got a error message: java.lang.IllegalArgumentException: contig must be non-null and not...
View ArticleHow is GQ calculated?
After reading "What is a VCF and how should I interpret it?" and "CalculateGenotypePosteriors", I've been left confused about how GQ is computed. The first article seems to clearly state that GQ is...
View ArticleGATK 4.0 will be released Jan 9, 2018
A long time ago in a galaxy far, far away, we started work on a brand new version of GATK in which the engine framework was to be completely revamped, streamlined and accelerated, with support for...
View ArticleMQ and Multisample calling from GVCFs
Dear GATK team, I'm getting puzzled with the MQ distribution coming out of our multisample calling. Our procedure is: We start form a set of GVCF files created with GATK 3.5 HaplotypeCaller in...
View ArticleCombineGVCFs warn messages into GVCF output??
Hi, I just switched to GATK 3.6 because of the bug in CombineGVCFs reported at http://gatkforums.broadinstitute.org/gatk/discussion/comment/31641#Comment_31641 I have noticed that now the CombineGVCFs...
View ArticleHaplotype caller BP_RESOLUTION :More AD values than alleles called for
My intention is to find different bases called in a particular chromosome location irrespective of it being assigned as SNP/badbase. I user the below command: java -jar 3.5/GenomeAnalysisTK.jar -T...
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Most of mapped reads are disappeared after Mutect2
Hi, I'm HJ.Kwon. I found some strange result from Mutect2 run. I'm analyzing Breast Cancer FFPE sample for research. In final vcf file, I couldn't find ERBB4's mutation which is already confirmed by...
View ArticleHC not calling variants at the edges after clipping probes
Hi, I am facing a strange issue with GATK 3.4. I have a set of PE fastq files. I first ran the variant calling pipeline using the following steps: bwa mem --> sam to bam --> mark duplicates using...
View ArticleGermlineCNVCaller: transition matrix priors
Hi, I'm giving the Beta GermlineCNVCaller a spin and downloaded the CN_transition_matrix files from the GATK bundle at...
View ArticleSNV gets dbSNP annotation in one sample, doesn't get annotated in another one
Hello everyone, I recently run HaplotypeCaller for GATK3.7 on a series of samples (several GATK runs performed at the same time), using the latest release of dbSNP(150). This was the command line I...
View ArticleError: Unable to retrieve result, with "VariantRecalibrator"
My command lines are as following: java -Xmx8g -jar $CLASSPATH/GenomeAnalysisTK.jar \ -T VariantRecalibrator \ -R $GenomeReference \ -input $InputVCF \ -nt 6 \...
View Articleabout mutect2 alt_allele_in_normal
Hi, I ran mutect2 with the default setting. And I got all of the mutations marked "alt_allele_in_normal". I just want to know if this is OK? Should it be some of the mutations marked alt_allele_in_tumor?
View ArticlegenotypeGVCFs vcf files empty, only the header
I'm running genotypeGVCFs on GATK 3.7/3.8, I tried both, but I'm only getting headers on the vcf files. I ran java -XX:ParallelGCThreads=4 -Xmx15g -jar GenomeAnalysisTKjar -T GenotypeGVCFs -R ref.fa -G...
View ArticleUsing GenomicsDBImport to prepare GVCFs for input to GenotypeGVCFs in GATK4
In GATK4, the GenotypeGVCFs tool can only take a single input, so if you have GVCFs from multiple samples (which is usually the case) you will need to combine them before feeding them to GenotypeGVCFs....
View ArticleJEXL filtering using criteria for groups of individuals instead of all single?
I have used JEXL-filtering to specify variable criteria for each normal in a cohort of control sample (for comparison to affected samples), like " -select ' vc.getGenotype("Normal1").isHomRef()...
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