Why did HaplotypeCaller report HET genotype for loci without reads supporting...
Hi GATK team, When I checked closely by IGV, I found many of the loci, with all reads supporting variants, were reported as a HET genotype by HC. After go back to the VCF result, I still don't...
View ArticleSome abnormal outputs of HaplotypeCaller
Hi GATK team, I found some abnormal output lines in VCF file which was generated by HaplotypeCaller in GATK 2.2.5 pipeline, with default parameters: 0/2 genotype reported for a bi-allelic loci: SCF35...
View ArticleIs this expected that HaplotypCaller identified 40% more variants by 2.2.5...
Hi GATK team, I recently downloaded GATK2.2.5 and re-analyzed a small part of my data which was analyzed by2.1.8 pipeline previously, following the same parameters. However I found the new pipeline...
View ArticleHaplotypeCaller Indel detection
We find the haplotypecaller is an excellent SNP caller. But recently we got confused for the indel results. We did the target sequencing (total 6 samples with 3 case vs. 3 control). We followed the...
View ArticleGenotyping a substitution using the HaplotypeCaller
Hi All, I have the following substitution that I am trying to genotype in a deep coverage (>1000x) dataset: 4 2558307 GCTGATGTGGGG GAGCTACTCAA I've aligned it using very relaxed BWA parameters and...
View ArticleHaplotypeCaller
I understand the HaplotypeCaller does some local assembly and realignment. Can someone expand on the parameters used during the local assembly? What is the kmer used for the assembly graph? I would...
View ArticleHow do I filter the reads that result in this type of error in some of my...
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Only one of refStart or refStop must be < 0, not both (-1, -8) Here is some information INFO 20:22:19,446 HelpFormatter - The Genome...
View Article15bp deletion previously called by GATK v1 not called by GATK 2.0 or 2.1
We have a 15bp deletion in a sample that was run on an Illumina sequencer twice: 1) on GAII, 76bp paired-end reads, 10-sample pool; 2) HiSeq2000, 100bp paired-end reads, 24-sample pool. Both times...
View Article"Cannot extend a symbolic allele" when running HaplotypeCaller on Picard...
I encounter this error when running HaplotypeCaller on picard-validated bam files using the b37 reference in the GATK resource bundle with GATK v2.3-4-g57ea19f. My commands are : -R...
View Articlewrong candidate haplotype chosen by HaplotypeCaller
I've been experiencing some apparent errors with HaplotypeCaller that I think could be related to how it chooses candidate haplotypes when performing multi-sample calling. Please see the example files...
View ArticleSensibility/sensitivity of VQSR processed VCF
Hi all, I've somewhere in this site that before VQSR the FP rate is expected to be around 10% (I guess for UnifiedGenotyper). Are there some updated statistics for VQRS? For HaplotypeCaller? For...
View ArticleHaplotype Caller incorrectly calling Blocks of Variants Heterozygous
Hi I seem to have found a bit of an issue with the Haplotype caller. Looking at variants called with it I've come across a number of small blocks in the genome where the Haplotype caller has called...
View ArticleUnifiedGenotyping, HaplotypeCaller and PhasebyTrasmission
Hi to all I began a variant analysis from 4 family related exome-seq samples in which a patology seems to be related to a polimorphism. I am just wondering which variant calling tools is better to use...
View ArticleBug in HaplotypeCaller v2.4: "Reads are too small for use in assembly."
We have received reports of a bug occurring with HaplotypeCaller in v2.4, with the error message "Reads are too small for use in assembly." We are working to fix it. In the meantime, if you encounter...
View ArticleRun time error during variant calling
Hi, I'm using GATK latest version to analyze paired end exome sequencing data. I'd like to see the SNP, Indel and also SVs. I have followed the workflow of GATK, from the duplicates marking to the...
View ArticleArrayIndexOutOfBoundsException in HaplotypeCaller
Command was: java -Xmx4g -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R ref.fasta -I sample1.cleaned.sorted.rmdup.realigned.bam -o sample1.haplo.vcf UnifiedGenotyper works with the same input...
View ArticleHaplotypeCaller 2.4
I am getting the following error. What is the minimum read size to do assembly? 50 basepair too short? ERROR stack trace java.lang.IllegalStateException: Reads are too small for use in assembly. at...
View ArticleBug in HaplotypeCaller 2.4-7 : "Bad likelihoods detected"
As reported here: http://gatkforums.broadinstitute.org/discussion/comment/4114#Comment_4114 If you encounter this bug too, please don't post a new question about it. Feel free to comment in this thread...
View ArticleIdentification of all SNPs in a haplotype based on a single SNP
Dear all! Is it possible to identify all SNPs in a haplotype using a single SNP? For example, input file: list of SNPs. Output file: list of all SNPs correlated with each SNP in the input file. Thanks...
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:...
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