mutect-1.1.7 stack error
I was looking at this post because it appeared to have the same problem that I am having http://gatkforums.broadinstitute.org/gatk/discussion/6054/stack-error-when-run-mutect-the-first-time ; however,...
View ArticleMemory error - Downsampling unavailable (3.5
Hi there, I am working on mitochondrial genomes (250 samples) with a coverage of ~7000x. The HC (v 3.5) is running perfectly for the firsts 248 samples but reaching the last ones, the following Java...
View ArticleAccurate ref/alt read counts for DNPs
Hi, I am using HaplotypeCaller in "genotype_given_alleles" mode in order to obtain REF and ALT read counts for candidate variants (using the AD field). This seems to work fine for SNPs and indels;...
View ArticleGATK variantsToTable output ordering of tumor and normal columns
Hi, I am using VariantsToTable to populate the vcf to a table. the vcf file was generated by： samtools mpileup -Q 20 -q 10 --skip-indels -f Homo_sapiens_assembly19.fasta -l ${merged_mutations} -v -t...
View ArticleDifferent file sizes ?
Hi GATK team, I have two questions about file size change. I just want to make sure there is no wrong in my pipeline. Our cluster sometimes kills several jobs without error message. I have recalibrated...
View ArticleBQSR and -L
I'm working with whole genome data (in a non-model with no databases of known sites), and I'm wondered if using -L to speed things up by running each chromosome in parallel creates a problem?...
View ArticleERROR: Code exception (see stack trace for error itself)
Hi GATK team, I am using VariantAnnotator in GATK release (3.4, 3.6, 3.7) with command-line: java -Xmx10g -jar $GATK -T VariantAnnotator \ -R $REF \ -V Input.vcf \ --resource:KGenomes...
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 ArticleDescription and examples of the steps in the ACNV case workflow
Once you have run GATK CNV, you can run ACNV for revised segments based on both the target-coverage profile and the ref/alt counts at heterozygous SNPs. ACNV will report estimates for the posterior...
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Errors about contigs in BAM or VCF files not being properly ordered or sorted
This is not as common as the "wrong reference build" problem, but it still pops up every now and then: a collaborator gives you a BAM or VCF file that's derived from the correct reference, but for...
View ArticleHard filters for Haplotype Caller
Hi team, (this is really two questions) Do you have any recommendations for hard-filtering haplotypecaller-generated vcfs ? This was my previous filter for the unifiedgenotyper output"...
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 ArticleSelectVariants Large VCF slow runtime
I am attempting to subset and filter a large (10k exome sample, 250GB) VCF file using SelectVariants. My goal is to subset by individual samples (iterating over each sample using a custom script and...
View ArticleThe number of times "Annotation will not be calculated..." warning is logged...
When running with an -nct value greater than 1, the number of times the warning message "HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper, not...
View ArticleRecommended protocol for bootstrapping HaplotypeCaller and BaseRecalibrator...
I am identifying new sequence variants/genotypes from RNA-Seq data. The species I am working with is not well studied, and there are no available datasets of reliable SNP and INDEL variants. For...
View ArticleCompiling GATK External Example
Hi so i'm using UBUNTU 14.04 with mvn 3.3.9 and i've cloned the GATK-protected from github. From the previous forum posts I'm not using the command `git reset --hard 3.1' and am using the raw gatk...
View ArticleGATK 3.7 HaplotypeCaller NullPointerException in...
HaplotypeCaller in GATK 3.7 (3.7-0-g56f2c1a) is throwing a NullPointerException in some cases. See below for log output from a failing run. It looks to me like the call to .get() in the...
View ArticleWhy I get insert size from CollectInsertSizeMetrics is less than read length?
Hi all, I used picard 2.8.1 to stat insert size in a bam file. The command I used is: java -jar /programs/picard.jar CollectInsertSizeMetrics I=/workdir/xz235/3T/282BAM/A6_HA5R1ADXX.bam...
View ArticleProblem with the hg38 bundle
Hi, I downloaded the hg38 bundle from: https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0/ When I aligned my data (BWM mem) to the fasta file...
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