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HELP: haplotypecaller doesn't call the driver oncogenic variant!
Hi, I'm using GATK haplotypecaller in order to detect varianti in a tumor sample analyzed with Illumina WES 100X2 paired end mode. I know KRAS p.G12 variant (chr12:25398284) is present in my sample...
View ArticleSupplying a bed file to GATK haplotype caller
Hello, I tried to find this option but I was unsuccessful. I would like to call SNPs only on a subset of my bam files, that is only on specific chromosomes. I have now done so by getting a subset of...
View Articlevcf file from a pooled sample
Hello, I am having difficulty in understanding the vcf output of haplotype caller when I use it for a pool of two individuals. I set ploidy to 4 in this case. When ploidy is 2, one get the heterozygote...
View Articlehaplotypecaller step took unusual long time
Hi, I have been using the best practices pipeline for illumnia samples for quite long time. Everything is fine. Recently, I am using the same pipeline for IONTORRENT samples. Everything is fine until...
View Articlegenotype calling in gatk
Excuse me: After calling the genotype using Haplotyper Caller in gatk, i manually check the reads covering the variant sites. But i found one exception: The genotype of one sample was 0/0，wild type,but...
View ArticleHaplotypeCaller on haploid genomes
I'm trying to run HaplotypeCaller on a haploid organism. Is this possible? What argument should I use for this? My first attempt produced a diploid calls. Sorry for the silly question
View ArticleWhen should I use HC in ERC mode?
Hi there, maybe this is a very basic question but, I've read several posts and sections of GATK Best Practices and tutorials but I can not get the point. What is the main difference between using GATK...
View ArticleHaplotypeCaller stopping midway without error, probably ram related
I'm running the HaplotypeCaller on a series of samples using a while loop in a bash script and for some samples the HaplotypeCaller is stopping part way through the file. My command was: java -Xmx18g...
View ArticleWhat is the best practice for calling/combining variants across multiple...
Hi, I am working with RNA-Seq data from 6 different samples. Part of my research is to identify novel polymorphisms. I have generated a filtered vcf file for each sample. I would like to now combine...
View ArticleWorkflow using HaplotypeCaller, GenotypeGVCFs, VQSR, and...
Hi, I have recal.bam files for all the individuals in my study (these constitute 4 families), and each bam file contains information for one chromosome for one individual. I was wondering if it is best...
View ArticleFiltering a variant on SOR that looks otherwise well supported
Hi, I need to apply hard filters to my data. In cases where I have lower coverage I plan to use the Fisher Strand annotation, and in higher coverage variant calls, SOR (using a JEXL expression to...
View ArticleHaplotypeCaller : Rod span ... isn't contained within the data shard without...
Hello, I have a pb with HaplotypeCaller. I saw that this error has been reported as linked with -nct option, but I did not use it. Strangely enough, I think my command worked some times ago (before...
View ArticleIncorrect AD values in HC-called vcf and combined gvcf
Hi, I am using GATK v3.2.2 following the recommended practices (...HC -> CombineGVCFs -> GenotypeGVCFs ...) and while looking through suspicious variants I came across a few hetz with AD=X,0....
View Article(howto) Call variants on a single diploid genome with the HaplotypeCaller
Objective Call variants on a diploid genome with the HaplotypeCaller, producing a raw (unfiltered) VCF. Caveat This is meant only for single-sample analysis. To analyze multiple samples, see the Best...
View ArticleHC_ERC output question:"sample1"
Hi there, This is maybe a silly question but I want to know if it is normal or not. I have just run HC in GVCF mode for each of my bam files. When I see the output...: CHROM POS ID REF ALT QUAL FILTER...
View ArticleHaplotype Caller output missing fileds AC/ AN
I'm a bit confused regarding the new GATK version and new HC-functions. I'm trying to call haplotypes in a family of plants. I call Haplotypes using haplotype caller, then I want to run Read-backed...
View ArticleHaplotypeCaller pooled sequence problem
Hi, I have a number of samples that consist of multiple individuals from the same population pooled together, and have been truing to use HaplotypeCaller to call the variants. I have set the (ploidy to...
View ArticleIllumina gVCFs
Hi GATK-ers, I have been given ~2000 gVCFs generated by Illumina (one sample per gVCF). Though they are in standard gVCF format, they were generated by an Illumina pipeline...
View ArticlegVCF files look different for same sample
Hi, I have noticed that every time I repeat a gVCF call on the same sample (~same Bam file), the output gVCF files are not exactly same. They are almost similar, but there will be a few differences...
View ArticleFinding exact reason for haplotype caller reassembly
I'm working on an association mapping project in a non-model bird (so there is a reference genome, but it may have problems). We're looking for SNPs linked to a phenotype using paired end GBS data and...
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