GATK v4.0.1.1 HaplotypeCaller
I am using GATK v4.0.1.1 HaplotypeCaller for variant analysis. (paired-end DNA sequenced data mapped to the reference using BWA mem). The command I used; “gatk HaplotypeCaller –R Reference.fna –I...
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...
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 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...
View ArticleDetecting called Indels with low read support on both sides?
Hi, I am mapping chimpanzee samples to the human reference hg19. I mappend the samples using the standard protocol (BWA mem, remove duplicates, indel realigner) and called them with GATK 3.7 Haplotype...
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...
View ArticlePloidy level in HaplotypeCaller in GATK 4.0
Hi, Thanks for the new version of GATK (GATK4.0). We have a pooling of 48 samples and the organism is diploid, we are using ploidy of 96 (48x2=96). earlier when I am using HaplotypeCaller for variant...
View ArticleCan 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 ArticleHaplotypeCaller does not filter duplicate reads, why?
Hi, Im running HaplotypeCaller on a server this way: java -XX:ParallelGCThreads=8 -Xmx80g -jar $GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -I a2tl1_14_final.bam --min_base_quality_score 25...
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 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 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 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 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...
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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...
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HaplotypeCaller may fail to detect variant with the same reads with a...
I have experienced a variant detection issue with confusion. The png file attached is the result of exact same NextSeq experiment but the read extraction range is different. NextSeq2_point.bam: bam is...
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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