Can I persuade GATK to resolve 2 indels as 3 SNPs?
I have the following two haplotypes in my data: ref: ATGAATA alt: ATTGAAA GATK is (not incorrectly) resolving this as an insertion of T after position 1 and deletion of T at position 6. However, I...
View ArticleError produced when running VariantAnnotator
Hi, I have begun getting the following error when running VariantAnnotator. What does this indicate? ERROR ------------------------------------------------------------------------------------------...
View ArticleBSQR and VSQR SNP and indel sites
Hello, to use these walkers, which files do you recommend using? I am currently using those shown below. Is this right? dbsnp_138.hg19.excluding_sites_after_129.vcf 1000G_phase1.indels.hg19.sites.vcf...
View ArticleReorderSam - inconsistencies between BAM and reference FASTA
Hi, I have a bam file aligned to the genome assembly 38 but I don't have access to the reference fasta used. I was runnig the HaplotypeCaller using another reference fasta and I got some errors...
View ArticleError with my HaplotypeCaller scala script
Hi everyone, I'm trying to run HaplotypeCaller through Queue because it really took a long time for HaplotypeCaller to finish one job. I've already read about some examples and forums to start on my...
View ArticleMESSAGE: Code exception (see stack trace for error itself)
Hi all, I meet some error while call variant with HaplotypeCaller, please help~~ Thanks a lot! my CMD: java -Xmx20g -jar GenomeAnalysisTK-3.6.jar -T HaplotypeCaller -R /human_g1k_v37_decoy.fasta -I...
View ArticleCoordinate errors
I'm trying to SVpreprocess some bam files but I keep getting errors stating that the bam files are not properly ordered: RCCache: Read coordinate chr22:23242120 precedes earliest allowed read...
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Variant Quality Score Recalibration (VQSR)
This document describes what Variant Quality Score Recalibration (VQSR) is designed to do, and outlines how it works under the hood. The first section is a high-level overview aimed at non-specialists....
View ArticleLeftAlign sites loose INFO field when using SMA
Hello, When using LeftAlignandTrim with GATK 3.6 I have run into the problem that the INFO field of split fields is not preserved. Instead the info field for all the the new sites is ".". This then...
View ArticleWhat are the standard resources for non-human genomes?
We're trying to put together some recommendations for folks who want to use GATK tools on non-human genomes. But we really don't have much experience with non-human genomes, so we're hoping that those...
View Articleabout the results from contEST
Dear Sheila, and Geraldine, would appreciate your input about understanding please the output from contEST that i run on normal-tumor pair : the results look in the following way (below) and the...
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What is a VCF and how should I interpret it?
This document describes "regular" VCF files produced for GERMLINE calls. For information on the special kind of VCF called gVCF, produced by HaplotypeCaller in -ERC GVCF mode, please see this companion...
View ArticleRead groups
There is no formal definition of what is a read group, but in practice, this term refers to a set of reads that were generated from a single run of a sequencing instrument. In the simple case where a...
View ArticleUnifiedGenotyper different results depending on the output mode
Hello I'm using GATK UnifiedGenotyper (v.3.6) for variant calling (extremely relaxed settings, no filtration). I found a false-negative variant (chr7:117188684T>G) that is clearly visible in IGV....
View ArticleDuplicate columns in ReadLengthDistribution
Hi GATK team, I've run the following command: java -jar gatk/3.6.0/GenomeAnalysisTK.jar -T ReadLengthDistribution -R /commun/data/pubdb/broadinstitute.org/bundle/1.5/b37/human_g1k_v37.fasta -L...
View ArticleJEXL Select of ANN in INFO field
I have a vcf file that includes annotations added with SNPeff. I would like to use SelectVariants to pull variant sites based on that annotation.The field is characterized as...
View ArticleStage 7 of CNVDiscoveryPipeline - all commands fail with...
I am attempting to run GenomeSTRiP's CNVDiscoveryPipeline. I have run SVPreprocess successfully and am now running CNVDiscoveryPipeline on a single chromosome. Each command at stage 7 fails with the...
View ArticlePicard Marduplicates error
Good day. I have encountered with this error while using MarkDuplicates tool. My task was killed then. The error message was: /appl/bio/picard/picard-2.6.0/bin/picard: line 5: 632 Killed \...
View ArticleVCF header with AD format 'Number=R' causes error in VQSR VariantRecalibrator...
I have a VCF header with the following number annotation for the AD field: ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">...
View ArticleLoss of Heterozygosity and the MNP variants
Hello, I searched around the forum but could not confirm --- whether the MNP annotation used by "SelectVariants" tool actually covers loss of heterozygosity (LOH) on a relative large genome region....
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