can i determine total count for a snp using HaplotypeCaller Tool?
Hello I am interested in finding the total number of reads supporting each snp found by the HaploTypeCaller tool. I just find the DepthOfCoverage tool which has the --countType COUNT_READS option. It...
View ArticleHow does HaplotypeCaller discriminate between heterozygous and homozygous...
Dear members of the GATK team I am using different GATK modules to detect some SNPs in my RNASeq data set. I did a test run for one individual to get an idea about the output of HaplotypeCaller. I know...
View ArticleHow to make results from GAT4.beta.3 "HaplotypeCaller" comparable to...
We have been using “UnifiedGenotyper” of GATK2.7 for SNV calling, with "EMIT_ALL_SITES" mode, which always generate great results. We recently learnt GATK4 is in-development, with UnifiedGenotyper...
View ArticleGenotypeGVCF on pooled data running out of memory despite providing 512GB to...
Dear GATK staff, I am doing SNP calling with GATK 3.8 on whole genome sequences of 12 pools (50 diploid individuals in each pool, genome size ~900 Mbp) of a non-model organism with scaffolded reference...
View ArticleRecommendations on using different versions of GATK for variant calling and...
Dear GATK Team, From what I understand, best practices recommend using the same version of GATK for variant calling (with HaplotypeCaller) and joint genotyping (with GenotypeGVCFs). Let's say, we found...
View ArticleI do not get the annotations I specified with -A
The problem You specified -A <some annotation> in a command line invoking one of the annotation-capable tools (HaplotypeCaller, MuTect2, UnifiedGenotyper and VariantAnnotator), but that...
View ArticleHaplotype Caller Makes SNPs look like INDELS
I'm using the HaplotypeCaller to look at SNPs related to antimicrobial resistance and am getting a result that looks like this: NC_011035.1 2049708 . CCGGCG C ... NC_011035.1 2049714 . C CAAGAA ... I...
View Articlewhat does the minReadsPerAlignmentStart argument in HaplotypeCaller mean?
The minReadsPerAlignmentStart argument in HaplotypeCaller is described as the minimum number of reads with the same alignment start for each location in an active region and has a default of 10. For...
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Haplotype Caller: too many alternative alleles found?
Hello gatk team, I am running HaplotypeCaller on 5 files of genomic alignments together at once. Despite the fact that I did a InDel realignment (Indel Realigner gatk) before running these files with...
View ArticleROD files out of FASTA? + other questions
Hey all, newbie here. tl;dr: I have a fasta file containing two sequences of my region of interest (~5.5 kbp), that differ in ~100 SNPs. What is the fastest way to generate a ROD file out of these...
View ArticleSegfault when running GATK 3.6 in a container
I'm using GATK on the DNAnexus platform, which can convert Docker images to the ACI format in order to run them. I have a Docker image that uses GATK 3.6 to call variants, which runs fine under...
View ArticleCRAM support in GATK 3.7 is broken
I have not been able to get GATK 3.7 HaplotypeCaller to work with CRAM files at all (it has a 100% failure rate so far with our whole genome CRAMs). Based on my analysis of the problem, I don't think...
View ArticleWhy is HaplotypeCaller spending 8 hrs on "Strictness is SILENT" step?
Hi, I am running HaplotypeCaller on whole genome re-sequenced (~10X coverage) African buffalo genomes, using a high coverage African buffalo genome as the reference (~90X). The genome is about 2.8Gb....
View ArticleIllegal argument exception when running HaplotypeCaller
Hello, One of my jobs is consistently failing to run HaplotypeCaller with the following error message: ERROR ------------------------------------------------------------------------------------------...
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Haplotype caller not picking up variants for HiSeq Runs
Hello, We were sequencing all our data in HiSeq and now moved to nextseq. We have sequenced the same batch of samples on both the sequencers. Both are processed using the same pipeline/parameters. What...
View ArticleProblem with allele specific annotation AS_QualByDepth (AS_QD) during variant...
Hi GATK team, First a big thank you for all your hard work in developing the tool and supporting the users! I am trying out the allelic specific(AS) annotations in version 3.6. While I have gotten a...
View ArticleGATK3 HC bug?
Hey GATK Devs! I'm writing to report some unexpected behavior on the part of GATK3.8 HC. I'm trying to use Illumina data to call SNPs and indels on a PacBio assembly and identify loci where assembly...
View ArticleHow to use HaplotypeCallerSpark from GATK 4 (beta 6) with Adam input files
Hi, it seems that GatkReads can read SAM/BAM/CRAM files and Adam files. But when I try to use HaplotypeCallerSpark with adam parquet files it fails because of some dictionnary validation ? Here's the...
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HaplotypeCaller can't call a 10bp deletion variant
Hi, GATK team. I use haplotypeCaller to call variants, but it can't find a 10bp deletion variant, as you can see in the graph. I use -L targetInterval -bamWriterType ALL_POSSIBLE_HAPLOTYPES -bamout...
View ArticleRegarding GenderMap file in genomestrip
Hello, Can someone tell me that what should i define gender for plant sample in gendermap file. Please explain me?? Thank you in Advance
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