per-sample DP is missing in called genotypes
I try to filter both variant non-variant sites together. I see the only reasonable way to do it is to filter by the per-sample DP. However, I noticed that substantial fraction of called sites (~10%)...
View ArticleWhat does one do with the raw VCF output of joint genotyping many gVCF files?
I have been following the best practices outline for calling SNPs on our samples, but I'm a little confused as to what to do with the VCF file produced following the joint genotyping/genotypeGVCFs...
View ArticleWhat does each data thread stand for in HaplotypeCaller
Hi, I'm using multi-threading for HaplotypeCaller by setting the nct option. But actually, I found that the speedup it gains isn't in proportional to the increase of the number of data threads. I tried...
View ArticleHaplotypecaller taking too long
Hi, When I run the pipeline according to best practices, HC on a fastq of 60MB (for a targeted panel) takes about 10 minutes, but then for the same pipeline/targeted region, on a fastq of 150MB, HC...
View ArticleHaplotypeCaller calling error
Dears, I found many calling errors like this, all of the phred quality >30, but HaplotypeCaller miss them, report as Homozygote. How to deal with it? Here is the code. Many thanks. java -Xmx200g...
View ArticleMemory error - Downsampling unavailable (3.5
Hi there, I am working on mitochondrial genomes (250 samples) with a coverage of ~7000x. The HC (v 3.5) is running perfectly for the firsts 248 samples but reaching the last ones, the following Java...
View ArticleHow to run GATK directly on SRA files
Hello , I recently saw a webinar by NCBI "Advanced Workshop on SRA and dbGaP Data Analysis" (ftp://ftp.ncbi.nlm.nih.gov/pub/education/public_webinars/2016/03Mar23_Advanced_Workshop/). They mentioned...
View ArticleUsing BAMOUT files to check HaplotypeCaller
In your documentation for this you say "You can see that the bamout file, on top, contains data only for the ActiveRegion that was within the analysis interval specified by -L. The two blue reads...
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Bug in HaplotypeCaller: GT is called 0/1, but AD is 206,0
HI, I'd like to report a weird result from HaplotypeCaller. We have a patient sequenced by targeted sequencing on HNF1B. This patient has been confirmed to have a whole gene deletion of HNF1B so we...
View ArticleVariant Calling in NGS data of a specific locus.
Hello, I'm rather new to variant calling and had a question regarding this process on NGS data performed on a specific locus. I sequenced the PCR amplicon of a bunch of samples in a pool together....
View ArticleIs there a paper describing the »Haplotype Caller algorithm?
Hi, I'd like to ask you if there is a paper describing the Haplotype Caller algorithm, if you could please send me the reference. I have tried to find it, but I only found the paper on GATK which is...
View Articlean error about HC call mutation genetoype and mutation type
Hi professor, when I use HC call mutations ，the genotype and mutation as follows: HC_Gene.refGene Chr Start End Ref Alt III17 HAVCR1 chr5 156479568 156479568 C CGTT,* 0/1 but when I chek the bam file...
View ArticleIs HaplotypeCaller suitable for use in a GWAS project?
Hi GATK Team, I'm performing a Genome Wide Association Study and have just used HaplotypeCaller to call SNPs. Having read previous threads discussing the reference bias inherent in HC (at least...
View ArticleWhy is Haplotype Caller not calling any variants?
Hi, I am following the BP guidelines for RNA Seq variant calling and am trying to run the Haplotype Caller on the output .bam files from the Split & Trim step. All the MAPQ scores of 255 have been...
View ArticleRGQ returning 0 for high numbers of aligned reads
Hi, Just wondering what the possible reasons could be for Haplotype Caller (version: 3.5-0-g36282e4) to declare a reference genotype quality of 0 for positions where the read depth is relatively high,...
View ArticleERROR MESSAGE: Graph must have ref source and sink vertices
Hello, I am running GATK 3.5.-0 and encountered the following error: ERROR MESSAGE: Graph must have ref source and sink vertices The error occurs towards the end of the file processing and the...
View ArticleHaplotypeCaller DP reports low values
Dear GATK Team, I've recently been exploring HaplotypeCaller and noticed that, for my data, it is reporting ~10x lower DP and AD values in comparison to reads visible in the igv browser and reported by...
View ArticleWhich variant caller should be selected for my dataset?
Hi, I am currently working on two different projects and interested in finding common and rare variants. Project1 - Organism : Influenza virus Number of samples : 18 Sequencing type: Exome sequencing...
View Articlereference allele with Haplotype Caller
Hi I'm trying to use Haplotype Caller for some WES and I used the --emitRefConfidence GVCF option in order to see only variants in my VCF output (no 0/0 homo wild type). Unexpectedly I obtained...
View ArticleHaplotypeCaller for a long time
Hi @Geraldine_VdAuwera I have many bam files obtained through best practices. I want to get gvcf for each sample, but it puzzled me that most samples finished the HaplotypeCaller (version 3.5) process...
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