problem with variant calling
Hi All, I am calling variants by using HaplotypeCaller, it runs with no error untill now, but the problem is the progress still on the percentage 44.6% from more than 30 hours until now. I have pasted...
View Articleproblem with variant calling
Hi All, I am calling variants by using HaplotypeCaller, it runs with no error untill now, but the problem is the progress still on the percentage 44.6% from more than 30 hours until now. I have pasted...
View ArticleOncotator output from 1.8 and 1.9
Are the 2 versions giving same output? The columns in the output files from the 2 versions are the same, right?
View ArticleArchived GATK 3.6
Where can I find the jar file for GATK version 3.6? Or when will it be added to the archive?
View ArticleRunning GenomeSTRiP to genotype results in Out of Memory Error
How is the java heap space increased in a queue script to run MergeGenotyperOutput ? I tried running the command with -Xmx6g parameter but the script ran with a heap space of only 2048m. When running...
View ArticleWhy DP in FORMAT filed can't be re-annotate base on input bam file by...
When I run VariantAnnotator by the follow command(GATK 3.6): java -Xmx8g -jar GenomeAnalysisTK.jar -R ./hg19.fa -T VariantAnnotator -I ./s733.RG.RA.RC.bam -A BaseQualityRankSumTest -A...
View ArticleIndel realignment for a normal-tumor pair of BAM files
Dear GATK team, I have noticed that sometimes, when I run IndelRealigner independently on a tumor BAM file and its matching normal BAM file, I get different haplotypes, leading to false somatic variant...
View ArticleError message using ReorderSam
Dear GATK team, I am still following the Best practice guide for SNP calling of RNA-seq data. For one of my samples, I obtained the following error message when applying the following program code:...
View ArticleMuTect2 output to Oncotator1.9
I use MuTect2 output vcf file as Oncotator input. The last 2 columns in vcf file is tumor and normal, and if I input this vcf file to Oncotator, then, oncotator gives 2 rows for each row in vcf file....
View ArticleOncotator1.9 Output
Where can I find any documentation for Oncotator1.9? What do the following variables mean? i_t_ALT_F1R2 i_t_ALT_F2R1 i_t_REF_F1R2 i_t_REF_F2R1 If these are same as another software:...
View ArticleHow does MuTect2 assign germline_risk filter
I have read MuTect1 paper and MuTect2 code, and it seems the germline risk is assigned this way 1. if variants in dbsnp, but not cosmic, the nlod cutoff is 5.5 2. otherwise, the cutoff is 2.2 Some of...
View ArticleGenotypeGVCFs will give a stack trace if using -nct > 1 and -allSites
Hi, I'm getting a NullPointerException (see trace below looks like some kind of NanoScheduler issue) when using GenotypeGVCFs and the -allSites argument when using more than one core via -nct. Running...
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Can I use GATK on non-diploid organisms?
In general most GATK tools don't care about ploidy. The major exception is, of course, at the variant calling step: the variant callers need to know what ploidy is assumed for a given sample in order...
View ArticleThe indel fraction is less than 20% but can be called in VCF as 50%
Hi GATK team, We used PCR amplicons to enrich the target genes, and sequence those targets with high depth, e.g., >1000X. Followed with GATK best practice, we applied several steps to call the...
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VariantAnnotator Exceptions
Hi GATK developers, I would like to run VQSR on my set of variants; however, they were called by samtools mpileup and bcftools. The error message from VQSR suggested me to run VariantAnnotator on my...
View ArticleVariantRecalibrator: ERROR stack trace
Hi, I am running the HaplotypeCaller v3.6 on a bunch of human exomes and all except one worked perfectly, this one crashes on chr15 and I couldn't figure out why, reads in this region look normal to me...
View ArticleIndel sizes Haplotypecaller can call
Hi, GATK developer I have a question about the size of insertions and deletions Haplotypecaller can call. More specifically, my sequence read is 150 bps and I would like to know the maximum indels...
View ArticleCollected FAQs about input files for sequence read data (BAM/CRAM)
1. What file formats do you support for sequence data input? The GATK supports the BAM format for reads, quality scores, alignments, and metadata (e.g. the lane of sequencing, center of origin, sample...
View Articlehaplotypecaller keeps crashing with OutOfMemory exception during -ERC GVCF mode
Hi, HC keeps crashing with java.lang.OutOfMemoryError for some samples not all of them during -ERC GVCF mode. I tried 5 samples but only two of them crashed. I've tried different heap sizes (like 8G,...
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...
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