Haplotype caller calling heterozygote with bad quality when it is Homozygote
Hi all, Second question of the day, I am sorry. I have been facing an issue that I saw many times on the forum but each time it seemed that you fixed it with new versions. Problem is I am using the...
View ArticleWhy GATK3.3 gives a more number (almost double) of INDELs than SNPs ?
I am working on Rice to call variants using GATK3.3. I have used BWA (bwa mem -M options) to map reads to reference genome. Followed by variant calling (HaplotypeCaller) by following Best Practices of...
View ArticleVariant calling of PacBio data using UnifiedGenotyper or HaplotypeCaller
We have PacBio data where we want to do variant calling. I tried both UnifiedGenotyper and Haplotype caller. I was not very successfull doing that. When I used UnifiedGenotyper I got some output, but...
View ArticleCannot retrieve file pointer positions in SAM file
Hello, I am receiving the following error. I am working with SAM files that were exported from CLC, then edited with Picard-tools to addReadGroups. I am not sure if I need to add an additional step to...
View ArticleSome sites that are overlapped by a spanning deletion getting a REF call...
It appears that there are some cases in which an upstream site is heterozygous for a deletion, and a downstream site should be heterozygous for something like 1/2 (where 2 is the * allele), but GATK is...
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 ArticleMissing DP field in Haplotype Caller produced vcf file
Hi, so I have some data that I ran through both Unified Genotype AND Haplotype Caller (because I wanted to see the difference in the number and quality of SNPs returned). I have merged both vcf files...
View ArticleHow to pass physical phasing information from HaplotypeCaller 3.4 through to...
Hi, I have been using HaplotypeCaller 3.4 on five hundred cattle genomes. I am wondering how to pass the physical phasing information, now generated by Haplotype Caller in N+1 mode, through...
View ArticleHaplotype Caller on SOLID samples reports less coverage per variant compared...
Hello Everyone! I'm using the whole GATK workflow to analyze Target Resequencing data coming from SOLID platforms. I followed the Best Practices for analysis and used the proper SOLID flags when using...
View Articleoutput_mode option in HaplotypeCaller using gVCF mode
Dear GATK team, I wish to get gVCF files for each data set. But I am not sure if I should still use --output_mode EMIT_ALL_SITES argument in my command lines. In your previous thread, I found you...
View Articlewonky vcf header :(
Hi, I've a problem with a VCF when combiningGVCFs, gatk/v3.4. "headerKey END found in VariantContext field INFO at chr2L:64003 but this key isn't defined in the VCFHeader" HaplotypeCaller -nct 30...
View ArticleERROR stack trace in ASEReadCounter
Hi, I was running ASEReadCounter and came across a "stack trace" error after completion of 14.1%. I am running the command like this: java -jar ../GenomeAnalysisTK-3.4-0/GenomeAnalysisTK.jar -R...
View ArticleHaplotypeCaller on mixed SureSelect and HaloPlex sets
I am preparing to run the Best Practices variant calling pipeline on a large set of samples. These samples were captured with several technologies, some with SureSelect, some with Nextera, and some...
View ArticleCohort calling-multiple samples as input
Hi GATK team, I was calling variants individually to generate gVCF files for each sample. Then I thought maybe I should also try using multiple samples as input from the ‘RealignerTargetCreator ‘ step...
View ArticleHaploytpeCaller gVCF calling for WGS
Hi, I am doing gVCF calls for whole genome samples and I would notice that the gvcf-calling jobs for some of the samples would fail at random genomic locations and if I resubmit those failed jobs, they...
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HaplotypeCaller lost 80% variants in a sample
Hi, We have several close-related samples each contain 3 million variants relative to the reference genome (both UG and HC give this results for most samples), while HC only give less than 1 million...
View ArticleHaplotype caller filter settings - Samtools called variant is filtered out...
Hi I am new to using HC. I am just using the HapMap sample NA12878 to validate my pipeline. I ran the following command on a BAM file that I generated. I noticed that certain SNPs were filtered out...
View ArticleWhy is this variant not called?
Hi there, I've been playing around with RNA-seq data and came across what seems to be a high quality single nucleotide variant but that isn't detected by HaplotypeCaller. I followed the Calling...
View ArticleProblem running GenotypeGVCFs for large all male cohort in chromosome X
Hi, I'm attempting to run GenotypeGVCFs on a cohort of ~4200 human male samples with targeted sequencing. I'm following the current DNA-Seq guidelines for cohort genotyping, with GATK v3.4-0. For each...
View ArticleGeneral variant detection pipeline
I'm a bit uncertain as to the optimal pipeline for calling variants. I've sequenced a population sample of ~200 at high coverage ~30X, with no prior information on nucleotide variation. The most...
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