Recommended protocol for bootstrapping HaplotypeCaller and BaseRecalibrator...
I am identifying new sequence variants/genotypes from RNA-Seq data. The species I am working with is not well studied, and there are no available datasets of reliable SNP and INDEL variants. For...
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Missing reference allele in GVCF file after running HaplotypeCaller
Hi, I used HaplotypeCaller in GVCF mode to generate a single sample GVCF, but when I checked my vcf file I see that the reference allele is not showing up: 22 1 . N <NON_REF> . . END=16050022...
View ArticleHaplotypeCaller: --min_base_quality_score vs -stand_call_conf and...
HaplotypeCaller has a --min_base_quality_score flag to specify the minimum "base quality required to consider a base for calling". It also has the -stand_call_conf and -stand_emit_conf that both of...
View ArticleAdding read filters to HC
Dear GATK Team, If I specify a read filter using the -rf option, is that read filter added to the filters applied by default, or will that then be the only filter that is applied (so I would also need...
View Articlenot all sites emitted with GENOTYPE_GIVEN_ALLELES
I am running HC3.3-0 with the following options (e.g. GENOTYPE_GIVEN_ALLELES): $java7 -Djava.io.tmpdir=tmp -Xmx3900m \ -jar $jar \ --analysis_type HaplotypeCaller \ --reference_sequence $ref \...
View ArticleHaplotypeCaller, StrandBiasBySample Annotation
Hello I am using GATK 3.3-0 HaplotypeCaller for variant calling. When I run HaplotypeCaller with the command java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R all_chr_reordered.fa -I 30_S30.bam...
View Article"GVCFs produced by HaplotypeCaller" vs "VCFs produced by UnifiedGenotyper...
Hi GATK team, i would like to seek opinion from your team to find the best workflow that best fit my data. Previously i've been exploring both variant calling algorithms UnifiedGenotyper and...
View ArticleSame setting, different SNPs being called
Hey, currently, I am working on 454 sequencing data. I am using GATK to call SNPs and indels, which works relatively well for the SNPs with the recommended filtering options. However, I was interested...
View ArticleBug? PairHMM outputs to stdout instead of stderr
Hi, I'm using 3.3-0-g37228af. This command gets around a feature that looks like a bug to me: gatk -T HaplotypeCaller -R ref.fa -I in.bam -o /dev/stdout 2> log.txt | grep -v -e PairHMM -e "JNI call"...
View ArticleCode exception at Haplotypecalle step.
Here is my command I actually used. java -jar -Xmx39g $gatk -T HaplotypeCaller -l INFO -R $reference -I $sample.bam --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000...
View ArticleHaplotypeCaller and ClippingRankSum
Is there any way to turn off the ClippingRankSum? When I attempt to use --excludeAnnotation ClippingRankSum it doesn't seem to do anything. I'm trying to locate the source of some inconsistencies...
View ArticleERROR : IndexOutOfBoundsException: Index: 3, Size: 3 in getAlternateAllele,...
Hi, I'm currently trying to use GATK to call variants from Human RNA seq data So far, I've managed to do variant calling in all my samples following the GATK best practice guidelines. (using...
View ArticleHC step 1: Defining ActiveRegions by measuring data entropy
This document describes the procedure used by HaplotypeCaller to define ActiveRegions on which to operate as a prelude to variant calling. For more context information on how this fits into the overall...
View ArticleHaplotypeCaller Multisample Variant Calling
Hey there! I've been using HaplotypeCaller as part of a new whole genome variant calling pipeline I'm working on and I had a question about the number of samples to use. From my tests, it seems like...
View ArticleHaplotypeCaller error: "Index: unable to reposition file channel of index file"
Is this likely to be something wrong with my bam.bai file? INFO 00:33:22,970 HelpFormatter - -------------------------------------------------------------------------------- INFO 00:33:22,975...
View ArticleHaplotype caller for SNP calling from RNA seq data
Hello, I have a general question. Why is it recommended to use single sample for SNP calling from RNA-seq data when using Haplotype caller? Isn't possible to provide all the samples together for the...
View ArticleDoes UG and HC downsample before or after exclusion of marked duplicates?
Does UG and HC downsample before or after exclusion of marked duplicates? I guess code is king for the answer...
View ArticleHaplotypeCaller on whole genome or chromosome by chromosome: different results
Hi, I'm working on targeted resequencing data and I'm doing a multi-sample variant calling with the HaplotypeCaller. First, I tried to call the variants in all the targeted regions by doing the calling...
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haplotye Caller
Hi I am using GATK version 3.3 (latest release) and following the best practice for variant calling. Steps i am using is 1. Run haplotye caller and get the gVCF file 2. Run GenotypeGVCF across the...
View ArticleWorkflow for fungal WGS
Hi all, I'm in a bit of a daze going through all the documentation and I wanted to do a sanity check on my workflow with the experts. I have ~120 WGS of a ~24Mb fungal pathogen. The end-product of my...
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