Error with the HaplotypeCaller when genotyping given alleles
Hi, I have a number of indels that were called using different methods (GATK UG and PINDEL mainly). I am now attempting to genotype them using the GATK HaplotypeCaller and am running into the following...
View ArticleHaplotypeCaller only generates header when called with recalibrated/dedupped...
Hello, I am having trouble calling variants using Haplotype Caller on simulated exome reads. I have been able to call reasonable-looking variants on the exome (simulated with dwgsim) with...
View ArticleHaplotypeCaller Incorrectly making Heterozygous Calls (Again)
Hi For GATK: GenomeAnalysisTK-2.4-7-g5e89f01 It would appear that the issue with the HaplotypeCaller making incorrect Het calls when it should be Hom has turned up again (if it ever actually went...
View ArticleBug in various tools, 2.4-7 : "ArrayIndexOutOfBoundsException"
As reported here: http://gatkforums.broadinstitute.org/discussion/2342/unifiedgenotyper-causes-arrayindexoutofboundsexception-3-how-to-fix-it...
View ArticleWhat is GGA mode?
In HaplotypeCaller, what is GGA mode? How is it different from normal mode?
View ArticleUnusual False Positives from HC/UG on edges of small, very high-coverage regions
Hey there, I'm currently working on a project that uses the MiSeq system to perform very deep sequencing (5000x coverage) on a small set of genes related to a particular cancer type. I have had some...
View ArticleVariant calling on Tumor samples (exome) - HaplotypeCaller or UnifiedGenotyper?
Hi there, According to your experience, what do you suggest for calling variants in tumor samples (exome) - HaplotypeCaller or UnifiedGenotyper? Have you seen any (major or minor) difference with both...
View ArticleRelease notes for GATK version 2.5
GATK 2.5 was released on April 30, 2013. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history Reduce Reads DRASTIC...
View ArticleHaplotypeCaller
Hi, I am adapting a two-year old pipeline, which includes UnifiedGenotyper to call variants. I would like to update this to the HaplotypeCaller. In the command for the UnifiedGenotyper there is an...
View ArticleProcessing raw SNP files
Hello, I have use Unified Genotyper and Haplotype Caller from GATK to do the SNP calling from my RNA-seq data. Now, I have the .vcf files generated by these two tools and I need to process them. I have...
View ArticlePatch for BadCigar filtering on Novoalign reads containing zero length CIGAR...
I'm running into a HaplotypeCaller issue with the latest release (2.5-2) using Novoalign input reads. Here's a small reproducible input file: https://s3.amazonaws.com/chapmanb/gatk_hc_problem_cigar.bam...
View ArticleHaplotypeCaller scattered job run time
Hi, I just managed to use HaplotypeCaller with the lasted version of Queue to call variants on 40 human exomes. The HaplotypeCaller job were scattered into 50 sub jobs and spread in our cluster with...
View ArticleHaplotypeCaller and Reduced Reads
Hi, I noticed that the statement "The interaction between the HaplotypeCaller and ReducedReads is still being worked out" is not in Guidebook of the lasted version (2.5.2) now. Does it mean that...
View ArticleHaplotypeCaller/UnifiedGenotyper produce no output
Hi, I'm using version 2.5-2 of GATK and until recently I was using version 2.3 of the Bundle. a few weeks ago I ran UnifiedGenotyper on WGS data (converted to Bam from Complete Genomics and processed...
View ArticleReference calls by HaplotypeCaller
Hi there, I'm trying to run the HaplotypeCaller in GATK2.5. I hope to get the confident reference calls as UnifiedGenotyper outputs, so I set the option "-out_mode EMIT_ALL_CONFIDENT_SITES". However, I...
View ArticleUG/HC interval list running start
GATK Team: This comment came up after some discussion with a colleague of mine: "If you split the human genome into 100 pieces, we have to create overlapping regions so that GATK won't miss variants,...
View ArticleHaplotypeCaller to call variants common between samples
Hi, I'm using HaplotypeCaller on a family that is unusual; it has two affected children and one unaffected parent. The disease is expected to be caused by a homozygous or compound heterozygous...
View ArticleHaplotypeCaller Error: Mismatch between the reference haplotype and reference...
Hi I have been running HaplotypeCaller on >700 monkey alignments and came across this error in some intervals: ##### ERROR...
View ArticleHaplotypeCaller Multisample Variant Calling
Hey there! I've been using HaplotypeCaller as part of a new whole genome variant calling pipeline I'm working on and I had a question about the number of samples to use. From my tests, it seems like...
View Articlewhy does it say : -stand_call_conf: command not found while after running...
this is my script: java -Xmx12g -jar /home/./programs/GenomeAnalysisTK.jar \ -R /home/./sas/hg19-1/ucsc.hg19.fasta \ -T HaplotypeCaller \ -I...
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