Phantom indels from HaplotypeCaller?
Dear GATK users and developers, I am running HaplotypeCaller followed by ValidateVariants and the latter complains about variants that have called alternative allele without any observation for it....
View Article9 Things You've Been Dying To Know About The HaplotypeCaller Paper
Q: What, there's a HaplotypeCaller paper? A: Yes! We are super pumped to announce the long-awaited release of The HaplotypeCaller Paper -- or rather, the preprint in bioRxiv. (Actually we announced it...
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 ArticleHow can I exclude snp sites with ALT asterisk by SelectVariants ?
Hello , I am using the latest GATK 3.6 to analysis my human WGS data. For snp analysis, when I ran VariantRecalibrator , it reported error as following: 1 788419 . A * 854.77 PASS DP=33 GT 0/1...
View ArticleVariantFiltration not filtering correctly
Hi, I'm running the following command to hard-filtering some variants: gatk -R /Users/debortoli/Doutorado/hg19/hg19.fa \ -T VariantFiltration -V vcf_no_indels.recode.vcf \ --filterExpression...
View ArticleMerge VCF with 1000 Genome Phase 3 VCF
Hi, I would like to merge my vcf with 1000 Genome Phase3 vcf. The issue for me is difference in chromosome position for the same data eg: RSID rs112185012 in my vcf is at "1:972645" and in 1000 Genome...
View Article#### ERROR MESSAGE: Writing failed because there is no space left on the disk...
Hello, I am getting this error when running my analysis with GenotypeGVCFs. I have enough size available so dont understand what the issue is. Script always stop at the same position. This is the...
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What is a GVCF and how is it different from a 'regular' VCF?
Overview GVCF stands for Genomic VCF. A GVCF is a kind of VCF, so the basic format specification is the same as for a regular VCF (see the spec documentation here), but a Genomic VCF contains extra...
View Article#### ERROR MESSAGE: Writing failed because there is no space left on the disk...
Hello, I am getting this error when running my analysis with GenotypeGVCFs. I have enough size available so dont understand what the issue is. Script always stop at the same position. This is the...
View ArticleError: Could not find or load main class...
I installed GenomeAnalysisTK-3.8-0-ge9d806836 with java version "1.8.0_151" to call variant by using SRR database. The command line i use that: $ java -cp "sra_gatk_package/*"...
View ArticleHaplotypeCaller does not filter duplicate reads, why?
Hi, Im running HaplotypeCaller on a server this way: java -XX:ParallelGCThreads=8 -Xmx80g -jar $GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -I a2tl1_14_final.bam --min_base_quality_score 25...
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Spanning or overlapping deletions (* allele)
We use the term spanning deletion or overlapping deletion to refer to a deletion that spans a position of interest. The presence of a spanning deletion affects how we can represent genotypes at any...
View ArticleReorderSam: Error "Invalid reference index -1"
I'm running java 1.8.0_25 and the latest version of picard tools to perform RNA-seq variant calling analysis. When I try to run ReorderSam, it says that the process is completed, but throws the...
View ArticleAllelic CNV (common snps and getbayesianhetcoverage
I created a list of common SNPs for GetBayesianHetCoverage following https://gatkforums.broadinstitute.org/gatk/discussion/7812/creating-a-list-of-common-snps-for-use-with-getbayesianhetcoverage. I...
View ArticleProblems in getting correct number of SNPs and INDELs in SelectVariant tool
Hi Everybody! I actually try to utilize a SelectVariant tool to separate my variants according to their types such as SNPs and INDELs in separate files respectively. After that i utilize the bcftools...
View ArticleMutect2 suggestion - option to output normal sites too
I'd like to see an option for Mutect2 that would allow input of a germline .vcf call file, and output to include all sites present in that file. The --output_mode option could be expanded to include an...
View ArticleJAVA comsol shell problem
I have a problem launching comsol program via xshell because of this. A fatal error has been detected by the Java Runtime Environment: # SIGSEGV (0xb) at pc=0x00007f759ac002b7, pid=11548,...
View ArticleProblems in getting correct number of SNPs and INDELs in SelectVariant tool
Hi Everybody! I actually try to utilize a SelectVariant tool to separate my variants according to their types such as SNPs and INDELs in separate files respectively. After that i utilize the bcftools...
View ArticlePhaseByTransmission does not phase any genotype
Dear GATK development team: Hi, I'm trying to use GATK to phase trio data. Below is the log that I copied, I filtered my PED file and VCF file so that both files contains the exactly same set of...
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