I am unable to use VQSR (recalibration) to filter variants
The problem: Our preferred method for filtering variants after the calling step is to use VQSR, a.k.a. recalibration. However, it requires well-curated training/truth resources, which are typically not...
View ArticleOrganizing pipeline for GATK
Hello all, I was wondering if there are any specially designed wrappers or organized pipelines for GATK, that allow you not to run each tool separately, provide log storage, error reporting, etc? I...
View ArticleClik here to view.
Related to snpEff
Hi @Sheila / @Geraldine_VdAuwera / team I would like to ask some question regarding to the snpEff using the input from GATK pipeline. A really fast intro about what we are doing; We currently in the...
View ArticleClik here to view.
DP in multiple sample SNP calling didn't match when viewed in alignment file
I did call SNP with three samples together and here is a line of vcf file: scaffold_1 67412 . A G 4591.64 PASS...
View ArticleHow to interpret GATK CNV call segment outcome?
After running through the workflow, call segment gives: Sample Chromosome Start End Num_Probes Segment_Mean Segment_Call 1 B62047 1 762414 196716563 8811 8.373648e-02 - 2 B62047 1 196744047 196801352...
View ArticleSNP calling for Haploid Genomes
Hello, I used both haploid version (-ploidy flag set to 1) and the default version of UG to call SNPs between a reference assembly and sequence reads that come from the same haploid genome. In the...
View ArticleHow to determine heterozygosity (hets) parameter for non human?
Hello, I would like to run the Haplotype caller on 3 samples of yeast. Is there a recognized value for the heterozygosity parameter for yeast (such as 0.001 for human)? and where can I find post...
View ArticleHaplotype Caller question
I have 2 questions - Where can i find documentation of what is -stand_emit_conf and -stand_call_conf, and what is the difference between two ? When i generate GVCF using --emitRefConfidence GVCF. The...
View ArticleUpdating Oncotator DataSources Using VCF files
Thanks for the help in advance. I am attempting to update my Oncotator data sources using vcf files. Below is my simplified command (i.e shortened dir and file names) python initializeDataSource.py...
View ArticleNegative read counts in Picard QualityYieldMetrics
Are negative values expected for TOTAL_READS, PF_READS and READ_LENGTH in QualityYieldMetrics? I'm guessing not. How I can track down the cause of this error then?
View ArticleHaploid SNP call in multi-samples: what filter to use for 100% alt allele...
I am calling SNPs for haploid organism. I used Haplotypecaller like this: $java -jar $gatk \ -T HaplotypeCaller \ -R Corca1_AssemblyScaffolds.fa \ -I cotton1_jgi.sam.bam.sorted.bam \ -o cotton1_raw.vcf...
View ArticleConsistant error seen in Picard 1.119
I have had a couple of enquiries over the last few days wrt this warning message that we are seeing a lot of: Java HotSpot(TM) 64-Bit Server VM warning: You have loaded library...
View Articleproblem with FastaAlternateReferenceMaker
Hi, I'm trying to use FastaAlternateReferenceMaker to generate an alternate reference from VCFs files. Unfortunately I get an error message: ERROR MESSAGE: Input files variant and sequence have...
View ArticleClik here to view.
Calling variants on cohorts of samples using the HaplotypeCaller in GVCF mode
This document describes the new approach to joint variant discovery that is available in GATK versions 3.0 and above. For a more detailed discussion of why it's better to perform joint discovery, see...
View Articlestr_contraction filter
We have an expected mutation filtered out due to "str_contraction" in mutect2. Are there any options to fine-tune this filter? If yes, what can be changed? thanks.
View Articledifference between Mutect 1.1.7 and MuTect2
Hello, I am trying to detect somatic Snps in a normal/tumour pair. I tried MuTect2 under Gatk (java -jar GenomeAnalysisTK.jar -T MuTect2) and varscan 2. To my surprise, there was very little overlap...
View ArticleVersion highlights for GATK version 3.6
What better way to start the summer than with a new GATK release? Umm no don't answer that, there's loads of good options. You could have a barbecue, eat some ice cream, go on a hike if that's the sort...
View ArticleProgressMeter 100% but the computation won't stop
Hi, I'm using chr21.fa as a reference genome to run the genomic pipeline so I can test my pipeline more quickly. The alignment ran smoothly but when I started to use GATK to do the realignment and base...
View ArticleIndel Realignment and BQSR ordering for somatic variant calling
Hi Broad folks, I'm in the process of constructing a genome analysis pipeline and have a question: In the picture here: (https://software.broadinstitute.org/gatk/best-practices/mutect1.php) you suggest...
View ArticleFully parameterized example workflow for somatic variant calling
Hi again GATK folks, Ya'll provide a lot of nice resources to get up and going with GATK, but what I can't find for the life of me is information on a functioning somatic variant calling pipeline where...
View Article