HaplotypeCaller misses a true variant
Hi, I'm updating my pipeline for exome sequencing analysis, so I'm experiencing the HaplotypeCaller capabilities! I have analyzed the same sample with the UnifiedGenotyper walker and the HC one and I...
View ArticleHaplotypeCaller sensitivity in large(ish) cohorts
One of my projects currently has ~150 patients (exomes) that I've been processing through the standard pipeline (2.8-1, including ReduceReads). In my most recent run through HC, I split the cohort in...
View ArticleMissing data in HaplotypeCaller
I have an issue with HaplotypeCaller and its use to call SNPs in RAD data. I recently used HaplotypeCaller to call SNPs in 600 samples + 50 subspecies samples. Worked fine. After adding more data to...
View ArticleHaplotype Caller giving error in chrUn_gl000225 region
Hi, We have used HaplotypeCaller for calling our whole genome sequencing data using hg19. Till now it called perfectly on every other chromosomes. But its giving an error message in chrUn_gl000225...
View ArticleWhy so many FP indels reported when running HaplotypeCaller on Indels for...
We ran a recent version of Haplotyper Caller on our SOLiD targeted resequencing data and got a ridiculous number of indels. We took a closer look at some and there was absolutely no evidence for an...
View Articleweird multisample output
Hi, I have run GATK Unified genotyper with multisample and I am getting unexpected output. (Hard filters used) Here are examples of the output format I get in the vcf for a sample:...
View Articlerunning haplotypeCaller using Queue
I wrote my first script in scala to run haplotyperCaller walker of GATK. However, I am running into some errors when I execute the *.scala script. I am unable to figure out the source of error, any...
View Articlerunning haplotypeCaller using Queue
I wrote my first script in scala to run haplotyperCaller walker of GATK. However, I am running into some errors when I execute the *.scala script. I am unable to figure out the source of error, any...
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Variant called if HC is run on individual bam but variant not called on...
Dear Team, I encounter a situation when ; If I run Haplotype caller on one .bam file - Haplotype caller called the mutation (sanger validated) java GenomeAnalysisTK.jar -T HaplotypeCaller -nct 15...
View ArticleWhat determines an active region? Different HaplotypeCaller results for small...
We observed a de-novo mutation identified by HC in a single trio that was not called when the same trio is included in a larger 95-sample cohort. The immediate cause seems to be that in the larger...
View Article--defaultBaseQualities in Haplotype caller
Dear Team, I'm getting the following error in Haplotype Caller (2.8-1): argument --defaultBaseQualities has value -1.00, but minimum allowed value is 0.0 while according to the CommandLine...
View ArticleRunning HaplotypeCaller with -nct
Hi! I am trying to see if I can speed up the HaplotypeCaller tool using the -nct flag. The GATK correctly identifies that my machine has 16 processors, and I specified that the HaplotypeCaller uses 16...
View ArticleRelease notes for GATK version 3.0
[A sneak peek at the upcoming release notes] GATK 3.0 will (hopefully) be released on March 5, 2014. Highlights are listed below. Read the detailed version history overview here:...
View Articlesame setting, different results (GATK...
When I run GATK with identical settings on some amplicon sequencing data from MiSeq (150KB region), I get different numbers of variants (approximately 10% difference), even after setting -dfrac to 1....
View ArticleNullPointerException in HaplotypeCaller for RNAseq
Hi, I was trying to call variants in RNAseq data using GATK 3.0 when I got the following stack trace: ##### ERROR...
View Articleusing haplotypecaller for 5.5mb of targeted capture across ~2400 bams
our group is calling variants using 5.5mb of targeted capture across ~2400 bams (for 830 subjects). i have successfully executed using unifiedgenotyper, but we would also like to run using...
View ArticleDisagreement between HaplotypeCaller, VariantAnnotator, and ValidateVariants...
I ran the HaplotypeCaller, VariantAnnotator, and Variant Validatoor on chr3 locations from a human tumor sample. The HaplotypeCaller command line is:...
View ArticleHC in gVCF mode gives error "Can only be used in single sample mode" when...
i have been using HaplotypeCaller in gVCF mode on a cohort of 830 samples spread over 2450 bams. the number of bams per sample varies from 1-4. for samples with <=3 bams, the routine works...
View ArticleWhy is HaplotypeCaller's '--emitRefConfidence' outputting 'NON_REF' in...
Hi, When using HaplotypeCaller's '--emitRefConfidence', with both GVCF and BP_RESOLUTION, we get lines like this one: 1 2337032 rs1129171 C T,<NON_REF> 480.77 ....
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HaplotypeCaller and detection of large indels
Hi, I am wondering about the detection of large indels with the haplotypecaller. I have an example where to my mind there is quite clearly a large deletion (a couple of kb) in the sample, but it is not...
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