Can GenotypeGVCFs be ran without filtering?
For bacteria genomes I use the "Best Practices" and the HaplotypeCaller to call variants. I would like to output a VCF containing all positions I can then parse on my own. I'm using -ERC BP_RESOLUTION...
View ArticleRecommended 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...
View ArticleMeaning of error: expected haplotypes.size() >= eventsAtThisLoc.size() + 1
Hi, I am running HaplotypeCaller (GATK 4.0.0.0) in genoype-given-alleles mode using a VCF of common coding germline variants. Please see the error below. Can anyone help to point me in the right...
View ArticleAny ploidy goes!
Until now, HaplotypeCaller was only capable of calling variants in diploid organisms due to some assumptions made in the underlying algorithms. I'm happy to announce that we now have a generalized...
View Articlerunning haplotypeCaller using Queue
I wrote my first script in scala to run haplotyperCaller walker of GATK. However, I am running into some errors when I execute the *.scala script. I am unable to figure out the source of error, any...
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I expect to see a variant at a specific site, but it's not getting called
This can happen when you expect a call to be made based on the output of other variant calling tools, or based on examination of the data in a genome browser like IGV. There are several possibilities,...
View Articlehaplotypecaller_gvcf_gatk4 failed to delocalize files
Hello, I was running haplotypecaller_gvcf_gatk4 for four samples in the same workspace. All but one finished the analysis. Message for the failed sample (all 50 shards) is as the following, Task...
View ArticleReadBackedPhasing of somatic and germline variants?
Hi all, I'd like to know which germline variants are proximal to and on the same chromosome as detected somatic variants. Is there an out-of-the-box way to phase germline and somatic variants to one...
View ArticleWhy I obtained a g.vcf with wrong variant DPs, and too few variants according...
Hi, I extracted Exome regions from public bam files to apply the same pipeline that I did for my samples and merge them. It is weird that looking in the g.vcf files, I have very few "variants", and...
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Using GATK: create a F0 SNP library and then genotype F2 sample using it
Hello GATK community, I would like your comments/suggestions for my strategy. I have F0 samples with two different phenotype. I have F2 samples with unknown phenotype. I would like to create a library...
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Haplotypecaller calls variants at a deletion region
Hi, I'm having a confusing problem when using haplotypecaller. Basically, I'm using haplotypecaller calling variants among more than 400 M. tuberculosis samples, sequenced with Hiseq2500 platform. I...
View ArticleSampleList annotation returns only one sample while being used in a variant...
Hi there, I have used HaplotypeCaller from GATK4 to call variants on two affected siblings. I put SampleList annotation in the command but only one sample is seen in all of the variants in the...
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Inconsistent results with HaplotypeCaller on haploid organism
Hello GATK team, I would appreciate some help in understanding how GATK works in GVCF mode on my data. Here is my data example I'm usign GATK v3.8: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 328-16...
View ArticleHaplotypeCaller in Gatk4 vs Gatk3.5
Dear colleagues, I noticed that latest "5 dollar pipeline" uses HaplotypeCaller from gatk3.5 not gatk4. Could you comment is it OK now to use HaplotypeCaller from gatk4 - if no, what are potential...
View ArticleHaplotypeCaller (gvcf mode) on whole genome vs chromosome by chromosome
I'm currently running my first real use of GATK. I was worried about running HaplotypeCaller on whole geneomes given some of the reports I've seen on these forums about how long it can take to run. In...
View ArticleHaplotypeCaller on sliced BAMs
Hello I'm trying to do germline calling using HaplotypeCaller. However, I'm only interested in obtaining germline variants for a subset of the genome. To save space and compute resources, I was hoping...
View ArticleSNP calling on inverted repeats
Dear GATK team, I have encountered a problem when I used the HaploTypeCaller for variant detection on about 100 plastid genomes. The plastid genome is haploid and contains two large inverted repeats...
View ArticleNullPointerException in HaplotypeCaller 4.0.1.1
Dear GATK team I am calling variants using HaplotypeCaller on both WGS data form a normal tissue samle and RNA seq data on tumor tissue. Settings for HC are slightly different for the RNA seq data but...
View Articleskip "indel realignment" and recalibration"
Hi to all can I skip "indel realignment" and re-calibration" steps, when I am using HaplotypeCaller ?
View ArticleCromwell: dead letters encountered
I am using Cromwell to run haplotypecaller-gvcf-gatk4.wdl. But it doesn't wok. Also docker is not invoked. [2018-03-24 15:55:59,90] [info] Running with database db.url =...
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