Multisample SNP Calling
Hello! I'm trying to use GATK to call SNPs on multiple bam files (at once) but I encounter some "problems". I tried HaplotypeCaller and UnifiedGenotyper and it works well. The vcf is generated. But not...
View ArticleAllele Depth = '0,0' and DP = '0' but the mutation was passed by filter
Hello, There is a question if anyone can explain to me how this variant calling was made, and why it was passed by filter. A variant information in filtered VCF is: 10 118265356 . G A 152.03 PASS...
View Article"GATK 4 ACNV Get Bayesian Hets Using Tumor and Normal for Capture" running...
Some of my samples on Firehose running the task "GATK 4 ACNV Get Bayesian Hets Using Tumor and Normal for Capture" failed due to what seems like memory errors. An example error log is below: Picked up...
View ArticleFastaAlternateReferenceMaker giving error
Hi, I am trying to run FastaAlternateReferenceMaker using an interval file but I am getting this warning whether I use the interval file or not. java -jar /local/scratch/aparihar/GenomeAnalysisTK.jar...
View ArticleClik here to view.
Get ready for ASHG 2016!
Tomorrow, a bunch of us are packing our bags and heading to Vancouver for the American Society of Human Genetics' Annual Meeting. We have a busy week ahead of us, between the GA4GH Plenary Meeting, the...
View Articleskip chromosomes GATK HaplotypeCaller
I am trying to use GATK HaplotypeCaller to identify variants on a set of bam files. however, my bam files contain only data on chrX, but the headers have the @SQ tag for all chromosomes, including the...
View Articleerror_java.lang.IllegalArgumentException: No data found--when using VQSR
ERROR ------------------------------------------------------------------------------------------ ERROR stack trace java.lang.IllegalArgumentException: No data found. at...
View ArticleTooldoc pages are blank
I have noticed the individual tooldoc pages are blank today. I have tested it with Firefox and Chrome, so I don't think it's a browser-related issue.
View ArticleMuTect2 seems to be hung, has created .vcf but run for many hours without...
I've had several instances of MuTect2 running, on 5 samples. Three have finished and there is a .vcf and corresponding .idx file for each, each pair with the same time stamp. The other 2 samples have...
View ArticleVariantFiltration documentation suggestion
In the VariantFiltration documentation of the --filterExpression option, make the word JEXL be a link to the JEXL documentation.
View ArticleIs VariantAnnotator compatible with the GVCF workflow?
Hi, In the Best Practices for Germline SNP & Indel Discovery in Whole Genome and Exome Sequence, https://software.broadinstitute.org/gatk/best-practices/bp_3step.php?case=GermShortWGS&p=2, the...
View ArticleHaplotypeCaller does not call variant depending on the interval list I use.
I am trying to explain why HaplotypeCaller calls a variant in some cases but not in others. I notice that a FN had very good coverage (>2000x) but wasn't being called. I ran HaplotypeCaller using an...
View ArticleRationale behind MuTect2
Hi ! I am trying to use MuTect2 on RNAseq data, trying to detect somatic mutation. I had a few interrogations about the formulas used by the program. I went through the original MuTect publication...
View ArticleVQSR: Bad input: Values for DP annotation not detected for ANY training...
Hi team, I'm have a vcf callset file generated using HaplotypeCaller in --emitRefConfidence GVCF mode with subsequent GenotypeGVCFs. I used the generated output.vcf file as input for...
View ArticleMutect2 with lastest nightly build problem
Hi, I am trying to run the variant calling step for the first time as a test. As I don't have any matched normal, I have only my tumour .bam file and a PoN composed of only 2 samples (for now). So I...
View ArticlePBS-DRMAA problems when I try execute Haplotyope-Caller
Good Morning, I'm trying to perform a parallel job using queue with a PBS scheduler but my script can't be executed. In particular, the script runs properly on a single node (so i won't attach the...
View ArticleI get very different MQ values when using GVCF vs BP_RESOLUTION
Hello! I had a question about the difference between using HaplotypeCaller's --emitRefConfidence GVCF vs BP_RESOLUTION. Maybe the answer is obvious or in the forum somewhere already but I couldn't spot...
View ArticleClik here to view.
The GATK Best Practices for variant calling on RNAseq, in full detail
We’re excited to introduce our Best Practices recommendations for calling variants on RNAseq data. These recommendations are based on our classic DNA-focused Best Practices, with some key differences...
View Articlepost-transcriptional modifications in RNA-seq base recalibration Best Practices?
Are the authors of GATK concerned about Post-transcriptional Modifications to mRNA negatively impacting Base Recalibration and Variant Calling via GATK RNA-seq Best practices? Reverse Transcriptases...
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 Article