Changing compression level in GATK 4.0.0.0
When running GATK 4.0.0.0, (in this case using Apply BQSR) the notice 11:36:10.430 INFO ApplyBQSR - HTSJDK Defaults.COMPRESSION_LEVEL : 1 appears. A bit of digging led me to the Python code in the...
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Calling variants on cohorts of samples using the HaplotypeCaller in GVCF mode
This document describes the new approach to joint variant discovery that is available in GATK versions 3.0 and above. For a more detailed discussion of why it's better to perform joint discovery, see...
View ArticleGATK4 Variant Recalibrator not recognizing format of...
The following error is observed when running VariantRecalibrator with the --truth-sensitivity-tranche argument. A USER ERROR has occurred: Argument truth-sensitivity-tranche has a bad value: [100.0,....
View ArticleCombining variants from different files into one
Solutions for combining variant callsets depending on purpose There are three main reasons why you might want to combine variants from different files into one, and the tool to use depends on what you...
View ArticleError produced when running VariantAnnotator
Hi, I have begun getting the following error when running VariantAnnotator. What does this indicate? ERROR ------------------------------------------------------------------------------------------...
View ArticleIs --downsample_to_fraction available for GATK 4.0?
Hi, Is their any equivalent flag to --downsample_to_fraction for GATK 4 (for example when running BaseRecalibrator)? Thanks
View ArticleGATK4.0 does not have the any more
I wander why the mulitple thread parameter [-nt ] has been cancer in GATK4.0? Or GATK 4.0 use a better way to replace the mulitple threads process, like using Spark?
View ArticleMutSigCV - Not enough mutations to analyze
I am running MutSigCV on GP in order to extrapolate significantly mutated genes in a cohort of 249 ovarian cancer FFPE samples after claiming 14472 mutations with targeted IonTorrent AmpliSeq on driver...
View ArticleCombineGVCFs - All alleles are missing
Hi, I am combining gcvf files into single gvcf files by chromosome, using CombineGVCFs, in order to run GenotypeGVCFs. When I checked the first gvcf file generated by CombineGVCFs, I noticed that at...
View ArticlePicard or GATK tools
Hi, some picard tools like MergeSamFiles were ported to GATK 4 beta. Now in the release version they are described as picard tools again. Even though they are part of the GATK and can be used as such....
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I expect to see a variant at a specific site, but it's not getting called
This can happen when you expect a call to be made based on the output of other variant calling tools, or based on examination of the data in a genome browser like IGV. There are several possibilities,...
View ArticleIntervals and interval lists
Interval lists define subsets of genomic regions, sometimes even just individual positions in the genome. You can provide GATK tools with intervals or lists of intervals when you want to restrict them...
View ArticleUnexpected result for VQSR with non-model organism (Plasmodium falciparum -...
Hi, I am variant calling wgs (~best practices; group calling for g.vcf) in Plasmodium falciparum and I would like to filter the call data using VariantRecalibrator VQSR, as opposed to setting hard...
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(How to) Call somatic mutations using GATK4 Mutect2
Document is in BETA. It may be incomplete and/or inaccurate. Post suggestions and read about updates in the Comments section. This tutorial introduces researchers to considerations in somatic short...
View ArticleDetecting called Indels with low read support on both sides?
Hi, I am mapping chimpanzee samples to the human reference hg19. I mappend the samples using the standard protocol (BWA mem, remove duplicates, indel realigner) and called them with GATK 3.7 Haplotype...
View ArticleSlow in running Genome STRiP
I have such issue for a while, but I am not sure whether this is just the nature of the Genome STRiP software. In the preprocessing step, at first multiple small jobs will be submitted to the queue,...
View ArticleDepth of coverage in GATK 4
Hello, I'm trying to find the depth of coverage for a targeted sequencing project using GATK 4, but I'm confused about which tool I can do this with. I've combed over the list of new tools and have...
View ArticlePicard RevertSam java.nio.file.NoSuchFileException
Hi, I'm starting to process a set of bams following the best practices and beginning from bams that were processed by someone else. Thus, I'm attempting to generate unmapped BAMs following this post,...
View Article50bp Reads
Hi, I am running 50 bp rnaseq reads through the RNASEQ best practice pipeline. 100% of my reads are being filtered. INFO 00:45:55,543 MicroScheduler - -> 50520046 reads (53.97% of total) failing...
View ArticleHow to combine GVCFs annotated by b37 (decoy) and hg19 reference genomes?
Hi GATK team, We have 2 GVCFs WES datasets. a) GVCFs ran using HaplotypeCaller with b37 decoy, b) GVCfs ran using HaplotypeCaller with hg19. We plan to combine all the GVCFs into 1 Master VCF, by doing...
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