About the haplotypes in hg19.fasta and the GTF file
Dear all, I am new to GATK and want to call variants for RNA-seq according to the best practice (https://software.broadinstitute.org/gatk/documentation/article.php?id=3891). I have three questions. The...
View ArticleGATK 3.7 and GATK 4 beta2
Dear team, I am using GATK 4 Beta2 for testing HaplotypeCaller for our NGS workflow. The command which I used is: time -p /gpfs/software/genomics/GATK/4b.2/gatk/gatk-launch HaplotypeCaller \...
View ArticleQuestion about BQSR
Hello! I have 100 samples and I followed the best practices. Every step is fine but when I was using the PrintReads it turned up to be an error. Version is 3.8 The commands I ran, $BWA mem -t 4 -aM -R...
View ArticleHow to resolve log4j version clash on SPARK
Hi, by default SPARK 2 has no support for log4j2. It uses Log4j 1.2.17. When I use GATK 4.0.0 build "as-is" (depends on Log4j2) all jobs on SPARK fail due to version clash. How this is supposed to be...
View ArticleVariantsToTable exxtract DP on mutect2 results
I want to obtain from vcf a table with position and DP. I try to use VariantsToTable but There is no wa tooobtin DP values. ##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense...
View ArticleClik here to view.
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 sequencing machine when it estimates the accuracy of each...
View ArticlePicard liftoverVCF error when attempting to liftover to build 38
Hi, Apologies for the Biostars cross-posting, but haven't received any replies there yet, so was hoping for some help. I've been trying to lift over .vcf files (human) from build 37 to build 38 using...
View ArticleCancer variant calling workflow with mutect and changes/additions to the GATK...
Hi all, I'm working on a cancer variant calling workflow (DNAseq) with MuTect as the variant caller, rather than HaplotypeCaller (due to it's low AF intolerance). I've gone through the forum and...
View ArticleClik here to view.
ERROR MESSAGE: Illegal base [ ] seen in the allele when running...
Hello everyone, It's me again Since I have finally worked through where to apply the parametre -trimAlternates, now I got another question. When I running FastaAlternateReferenceMaker, I got the error...
View ArticleJoint Genotype calling using Genotype GVCF: Possible solution/approach for...
Hi Geraldine I have WGS data on over 1500 samples. Currently the structure of files is: Group of 200 sample in each gVCF. Then the each gVCF is divided per chromosome and further division is done by...
View ArticleMemory problem with HaplotypeCaller -L
Morning, I´m using HaplotypeCaller program spliting by chromosomes in sheep genome. On 22 chromosomes the process has been completed correctly, but on the others there have been several errors. The...
View ArticleIs it useful to call LeftAlignIndels after IndelRealigner
Hi, In my pipeline to find variants in bacterial genome, I am first calling IndelRealigner and then calling variants using HaplotypeCaller. As left aligning of indels seems to be an important step,...
View ArticleDepthOfCoverage GATK4
Back in the day, I used to have a list of bam files (bam.list), a list of exome targets (targets.bed), a reference (ref.fa) and I could get per-sample coverage depth summary in GATK3:...
View ArticleGenomicsDB
GenomicsDB is a datastore format developed by our collaborators at Intel to store variant call data (where "datastore" = something that we mere mortals can think of as a database, even though IT...
View ArticleClik here to view.
Human genome reference builds - GRCh38/hg38 - b37 - hg19
This document covers the specifics of human genome reference assemblies. For more general information about reference genomes, including definitions of specialize terms used here, please see the...
View ArticlePicard: FixMateInformation crash
Hello, I was asked to re-post this question here. It was originally posted in the Picard forum at GitHub at https://github.com/broadinstitute/picard/issues/161. Regards, Bernt ORIGINAL POST (edited)...
View ArticleGATK4 realignment
As discussed in a blog post, GATK4 removes the realignment step: As announced in the GATK v3.6 highlights, variant calling workflows that use HaplotypeCaller or MuTect2 now omit indel realignment. This...
View ArticleGenotypeGVCFs error
Hi I am getting the following error. I ran the exact same samples/pipeline a couple of weeks ago using 3.6 and it worked fine, now with 3.7 I am getting an error: INFO 09:49:49,742 HelpFormatter -...
View Article[GATK 4.0.0.0] CollectRnaSeqMetrics --IGNORE_SEQUENCE as required argument?
Hi, I have been using an old version of PicardTools for some time and I have only recently decided to move to GATK4, mostly due to the improvements in performance. Upon doing so I have noticed that...
View ArticleClik here to view.
Strange behaviour (bias?) in BaseRecalibrator
Hello, I would like to report a possible weird behaviour of GATK BaseRecalibrator. During my analyses I follow the suggested "Best Practices", so after aligning I mark the duplicates (if needed) and...
View Article