Dramatic decrease in the number of variants discovered after applying --ploidy
Hi! I did two haplotypecaller GVCF runs on DNA-Seq data, one with default ploidy 2 and one with ploidy 28 (my library is a pool of 14 diploid animal samples). I noticed there is a drastic decrease in...
View ArticleGATK HaplotypeCaller does not forward @PG BAM header lines to -bamout
Hey GATK Devs! I'm using GATK (v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18) to call SNPs and Indels on a single sample. The reads were aligned with BWA (v0.7.12) and duplicates marked with Picard...
View ArticleCan the results of UnifiedGenotyper and HaplotypeCaller be significantly...
Hi! I'm trying to replicate the variant calling procedure done by a previous graduate student in my lab. To be precise, I have access to the original fastq files and his final vcf file; unfortunately,...
View ArticlePhasing SNPs and Indels
Hi I was looking into tools for phasing indels and SNPs. It seems that ReadBackPhasing only supports phasing of SNPs. I'm working on data from TCGA, and according to your docs HaplotypeCaller which can...
View ArticleError running haplotypecaller (v3.3)
I am running the haplotypecaller on multiple samples all but one work correctly with the following commands, however one is resulting in a binary file instead of the gvcf. Any suggestions how to fix...
View ArticlePhasing with HC
Hi I'm currently calling variants using HaplotypeCaller on different subsections of a WGS file (<5Mbp). The number of phased variants that show up are very low. How can I increase the 'yield' of...
View ArticleA 50 bp insertion (INDEL) varaint calling
Hi All, I am using both UnifiedGenotyper and HaplotypeCaller to genotype given alleles from amplicon based sequencing data. It seems that both caller did not performe well on variant rs1799752, a 50 bp...
View ArticleHaplotype Caller caller error in GATKv3.6
Hi, Sample is NA12878 and HC runs on this sample routinely as part of our testing. This runtime error seems to be sporadic. ERROR MESSAGE from HC is below INFO 14:08:15,398 ProgressMeter - 16:28875483...
View ArticleHaplotypeCaller not calling variants overlapping with active region and...
We've been running regression tests of HaplotypeCaller against previous UnifiedGenotyper output and we found a locus where UG originally called a set of 4 low allele balance SNPs while HC produced no...
View ArticleSingle-Sample Genotyping: Different Workflow?
Hi, If I need to independently call and genotype a single sample, is there a different workflow or set of GATK tools and settings that I ought to use instead of using haplotypecaller to generate a GVCF...
View ArticleDuplicate Key Error in GATK4 Haplotype Caller
Hello, I have been trying to resolve an issue that occurred in some of my samples while running GATK4 Haplotype Caller. After the program has been running for a while, it suddenly stops and this error...
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Impact of VQRS variant set size on model
Hi, We are evaluating the option to gather a set of 'good reference samples' to function as additional data in the VQRS step during WES analysis. We would like to do so, since we receive trio-based...
View ArticleHaplotypeCaller and GenotypeGVCFs sensibility on heterozygous variants
Hello, I recently compared results from GATK best practices (bwa, Picard, HaplotypeCaller, GenotypeGVCFs) with a snp array set (a high confident known variant detection method) for 6 samples (data from...
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What is a GVCF and how is it different from a 'regular' VCF?
Overview GVCF stands for Genomic VCF. A GVCF is a kind of VCF, so the basic format specification is the same as for a regular VCF (see the spec documentation here), but a Genomic VCF contains extra...
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Bug: HaplotypeCaller -drf
If I call HaplotypeCaller with --help it says that with -drf I can name "read filters to disable". Notice the plural. So I assume disabling multiple filters must be possible somehow. I'm trying to find...
View ArticleHaplotypeCaller: INFO report -> odd values
There are 68 reads covering my SNP of interest: samtools view mybam.bam 6:1611802-1611802 | wc -l 68 This matches what I see in IGV (after turning off all the filters in the preferences of course!)....
View Articlesome questions about difference between HaplotypeCaller and MuTect2
Hi, Recently I have been worked in variant calling using GATK and I have some questions in the process of learning GATK tools. Iām interested in the essential difference between HaplotyepCaller and...
View ArticleReference Confidence Mode
Hi Is a benefit of using joint genotyping in reference confidence mode a more accurate genotype for samples, especially non W Eurasians (when using NA 12878 as the reference) ?
View ArticleWhy I can not reproduce my result on different hostcomputer?
Dear colleague, I have encounter a strange issues with GATK-3.3/3.7: I used HaplotypeCaller to call variants on the same realn.recal.bam file, and it gave me different results when i ran on different...
View ArticleVariant in VCF of multiple samples called by HaplotypeCaller absent in their...
Hello GATK team, I followed GATK best practices and called variants with haplotypecaller in 6 exome samples. However, in 4 patients (total) I have a variant on Chr12 that is absent in the BAM file. the...
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