What is GGA mode?
In HaplotypeCaller, what is GGA mode? How is it different from normal mode?
View ArticleHaplotypeCaller only generates header when called with recalibrated/dedupped...
Hello, I am having trouble calling variants using Haplotype Caller on simulated exome reads. I have been able to call reasonable-looking variants on the exome (simulated with dwgsim) with...
View ArticleVariant calling on Tumor samples (exome) - HaplotypeCaller or UnifiedGenotyper?
Hi there, According to your experience, what do you suggest for calling variants in tumor samples (exome) - HaplotypeCaller or UnifiedGenotyper? Have you seen any (major or minor) difference with both...
View ArticleHaplotypeCaller - single block subsitution or multiple SNVs?
Hello GATK team, I notice that HaplotypeCaller will sometimes call a single block substitution variant where UnifiedGenotyper would call two separate SNVs, e.g.: HC chr12 93147901 . CGTGCCA TGTGCCT...
View ArticleHaplotypeCaller
Hi, I am adapting a two-year old pipeline, which includes UnifiedGenotyper to call variants. I would like to update this to the HaplotypeCaller. In the command for the UnifiedGenotyper there is an...
View ArticleHaplotypeCaller/UnifiedGenotyper produce no output
Hi, I'm using version 2.5-2 of GATK and until recently I was using version 2.3 of the Bundle. a few weeks ago I ran UnifiedGenotyper on WGS data (converted to Bam from Complete Genomics and processed...
View ArticleHaplotypeCaller rs annotation
Hi there, I'm running now the new GATK 2.2-2 version and I noticed an issue with HaplotypeCaller I had in the previous version I was using. Despite adding the dbSNP ROD to the walker, the emitted VCF...
View ArticleReference calls by HaplotypeCaller
Hi there, I'm trying to run the HaplotypeCaller in GATK2.5. I hope to get the confident reference calls as UnifiedGenotyper outputs, so I set the option "-out_mode EMIT_ALL_CONFIDENT_SITES". However, I...
View ArticleUG/HC interval list running start
GATK Team: This comment came up after some discussion with a colleague of mine: "If you split the human genome into 100 pieces, we have to create overlapping regions so that GATK won't miss variants,...
View ArticleHaplotypeCaller to call variants common between samples
Hi, I'm using HaplotypeCaller on a family that is unusual; it has two affected children and one unaffected parent. The disease is expected to be caused by a homozygous or compound heterozygous...
View ArticleHaplotypeCaller Error with ReduceReads Exomes
Hello dear GATK Team, when trying to run Haplotypecaller on my exome files prepared with ReduceReads i get the error stated below. As you can see the newest GATK Version is used. Also UnifiedGenotyper...
View ArticleRelease notes for GATK version 2.2
GATK release 2.2 was released on October 31, 2012. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history Base Quality...
View ArticlePatch for BadCigar filtering on Novoalign reads containing zero length CIGAR...
I'm running into a HaplotypeCaller issue with the latest release (2.5-2) using Novoalign input reads. Here's a small reproducible input file: https://s3.amazonaws.com/chapmanb/gatk_hc_problem_cigar.bam...
View Articlewhy does it say : -stand_call_conf: command not found while after running...
this is my script: java -Xmx12g -jar /home/./programs/GenomeAnalysisTK.jar \ -R /home/./sas/hg19-1/ucsc.hg19.fasta \ -T HaplotypeCaller \ -I...
View ArticleHaplotype caller, multisample calling on set of 9 solid and 1 ilumina sample
How does the haplotype caller handle multiple samples? Does it do a local denovo assembly for every sample and then compare those or does it do 1 local denovo assembly using the reads of all the...
View ArticleHaplotype Caller -dcov flag
Is there any way to override/re-implement the -dcov flag (which has been removed from the haplotype caller). I have a region that is almost 700 base pairs deep and continually causes a memory overload...
View ArticleHow does HaplotypeCaller identify potentially variable regions?
Hi there, I'm starting to use use the HaplotypeCaller to identify variants in my exome projects, but I was wondering how it initially determines if a region has the potential to be variable. I couldn't...
View ArticleCalling only some positions
Hi, I'm trying to use GATK to validate reproducibility of the NGS part. We run the same sample 3 times on a MiSeq and I have a list of positions and I want to see if GATK has the same calls in all...
View ArticleHaplotype caller
Dear Team, i am using Haplotype caller to identify the indels in my sequence.. i am running it in command line.. java -jar...
View ArticleHaplotypeCaller could not produce HaplotypeScore in raw.vcf file
Hi, Iām trying to use GATK(2.6-4) HaplotypeCaller for variant calling as follows: java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R hg19/ucsc.hg19.fasta -I...
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