CombineGVCF: java.lang.ClassCastException: java.lang.Integer cannot be cast...
Hi I'm trying to combine a bunch of gvcf's generated by bcbio-nextgen with GATK. However, when running the command I get the following error: INFO 09:32:20,508 GenomeAnalysisEngine - Preparing for...
View ArticleRead Groups without known barcodes
Dear all, I am working with some barley accessions but the barcodes for the samples are not known (not publicly available). However, because the addition of the read groups is a prerequisite for BQSR...
View ArticlePicard - SortSam
Hello, I'm using Picard's SortSam tool and was wandering if I can use the same script for 2 files? Meaning, can I do something like that (script below)? What would be the separator sign? Or I would...
View ArticleAre filtering and trimming necessary before mapping and SNP calling using GATK
Hi GATK team, I am using GATK to call SNPs from whole genome re-sequencing data. According to FastQC report, base quality was lower than 20 after 100bp (120bp reads) and illumine Universal Adapter...
View ArticleWeb-based Oncotator server
There is a web-based version of Oncotator which you can use for annotation without running anything on your own machine. However, please note that the web-based version is an older version, with fewer...
View ArticleBAM with soft-clipped primer sequences as an input for RevertSam (Tutorial...
Could I use RevertSam on primer-clipped BAM and then MergeBamAlignment using the primer-clipped BAM and uBAM originated from it as input? I'm analyzing paired-end TruSeq Custom Amplicon panel data,...
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VQSR: low TiTv
Hi I'm trying out VQSR on a batch of 16 human whole genomes (~25-30x). I was wondering if someone could review the below profiles. It seems the false-positive rate is much higher than the GATK...
View ArticleGATK4 resource bundle
Hi, I was wondering if you guys are planning to release a new resource bundle with full hg38 support (+patches)? Perhaps to celebrate the release of GATK4? Thanks M
View ArticleMergeBam giving error although the inputs are sprted
I am trying to use picard merge bam, after I sort the alignments and unaligned reads wrt queryname using picard. I merge them with SORT_ORDER=queryname Then I get the following error: Exception merging...
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Calling variants in RNAseq
Overview This document describes the details of the GATK Best Practices workflow for SNP and indel calling on RNAseq data. Please note that any command lines are only given as example of how the tools...
View ArticleHow to use HaplotypeCallerSpark from GATK 4 (beta 6) with Adam input files
Hi, it seems that GatkReads can read SAM/BAM/CRAM files and Adam files. But when I try to use HaplotypeCallerSpark with adam parquet files it fails because of some dictionnary validation ? Here's the...
View Articleobsolete index parameters
Hello, We have a bunch of gVCFs created with an older version, when the flags -variant_index_type LINEAR -variant_index_parameter 128000 --filter_mismatching_base_and_quals were still necessary for...
View ArticleFiltering MuTect2 output for depth of coverage
Dear GATK team, I am writing with a question about depth of coverage in the output of MuTect2 (GATK3 and GATK4). I would like to filter my somatic calls to keep only calls with sufficient depth of...
View ArticlePL
Hi, I realize PL will be normalized in this page. https://www.broadinstitute.org/gatk/guide/tagged?tag=pl However, I need the data before normalize, raw PL, where can I get it? Thanks for your help....
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HaplotypeCaller can't call a 10bp deletion variant
Hi, GATK team. I use haplotypeCaller to call variants, but it can't find a 10bp deletion variant, as you can see in the graph. I use -L targetInterval -bamWriterType ALL_POSSIBLE_HAPLOTYPES -bamout...
View ArticlePicard GenotypeConcordance
Hi GATK team! I have a question. I want to compare my two VCF files for checking the discordance. Reading the GATK Forum, I picked up picard Genotype Concordance. I can get the metric files, but I...
View ArticleHow to run the entire pipeline (using even Spark tools) from Java?
I am trying to write a Java pipeline which follows the GATK Best Practices, in particular, using more than one input sample. As first steps, I am trying to use FastqToSam (even if not mandatory for the...
View ArticleUsing GenomeStrip to genotype known vcf
Hi, I want to genotype known CNVs (from 1000G Phase3, GoNL, etc.) in our samples using GenomeStrip without performing any discovery step at first. 1) Do I have to run only the SVPreprocess steps...
View ArticleUsing JEXL to apply hard filters or select variants based on annotation values
1. JEXL in a nutshell JEXL stands for Java EXpression Language. It's not a part of the GATK as such; it's a software library that can be used by Java-based programs like the GATK. It can be used for...
View ArticleVQSR error
I used to run VQSR using the following command. Approximately for 400 samples it worked very well. But for the first time I am getting an error while doing VQSR by adding few more sample with old ones....
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