HaplotypeCaller can not emit bamout in multi-threaded mode
Hi all, I used multi-threading mode on HaplotypeCaller hoping to save some time. But seemed like bamout can not be emitted in multi-threading mode. I searched the answers. But I am still not sure if...
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What is a GVCF and how is it different from a 'regular' VCF?
Overview GVCF stands for Genomic VCF. A GVCF is a kind of VCF, so the basic format specification is the same as for a regular VCF (see the spec documentation here), but a Genomic VCF contains extra...
View ArticleAD in VCF doesn't match BAM
Hello, I'm using GATK to call variants in my RNA-Seq data. I'm noticing something strange, perhaps someone can help? For a number of sites the VCF is reporting things I cannot replicate from BAMs. How...
View ArticleThe Splitting of BAM file (RNA-seq) before calling variants is throwing error
First of all I thank for the Tool , I am using this GATK var calling for my RNA-seq data.. I have been following the commands said in the site but its stopping me at the splitting BAM file step with...
View ArticleProblems with dbSNP file using the HaplotypeCaller
Hi, I am having the following problem: I use the HaplotypeCaller (GATK 3.3.0) for variant calling. To identify variants that are known according to dbSNP, I use the "--dbsnp" statement and define a...
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Variant calls being missed - how to improve variant detection using Sanger...
@Geraldine_VdAuwera and @Sheila - Please help! I've read through many of your posts/responses regarding HaplotypeCaller not calling variants, and tried many of the suggestions you've made to others,...
View ArticleThe VCF file generated by GATK HaplotypeCaller does not contain SOR information.
I am using GATK HaplotypeCaller to call variation with the following command: java -Xmx20g -jar GenomeAnalysisTK.jar -l INFO -R hg19.fa -T HaplotypeCaller -nct 16 -I D-2.realigned.recal.bam -I...
View ArticleHaplotypeCaller bugs
Hi, I have tried to solve several issues which came up while trying to run the HaplotypeCaller. For this one, I didn't find anything on google and to be honest when pasting the error, google doesn't...
View ArticleHaplotypeCaller DP reports low values
Dear GATK Team, I've recently been exploring HaplotypeCaller and noticed that, for my data, it is reporting ~10x lower DP and AD values in comparison to reads visible in the igv browser and reported by...
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Periodicity in variant calling quality - is this normal?
After applying the standard RNA-Seq pipeline (with STAR, etc) I called varients with the command: java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R chromosome.fa -I ./final.bam...
View ArticleHaplotypeCaller Error: Mismatch between the reference haplotype and reference...
Hi I have been running HaplotypeCaller on >700 monkey alignments and came across this error in some intervals: ##### ERROR...
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Haplotype Caller calls variants where there are no reads?
Basically, i'm seeing variants called where I have no reads. Not sure why, but maybe the developers might know why? All the data needed to replicate this can be found at...
View ArticleHaplotype caller for RNA-seq
Hi, I am trying to call SNPs from RNA-seq data. The data that I have is a pooled sample (from the larvae of shellfish 1000s of larvae pooled together to get enough RNA) I have 6 of those samples. Can I...
View ArticleHaplotypeCaller report different genotype on the same location with different...
Hi GATK team, I am using the GATK 3.3 HaplotypeCaller. I found if i use different -L i will have different genotype on the same location. My para is very simple: -T HaplotypeCaller -R ucsc.hg19.fasta...
View ArticleHaplotypeCaller doesn't call true variants which are located on the outside...
Hi, I was running the haplotypeCaller for many samples, but some variants (validated as true positives by using other techniques) within these samples are not called by the haplotypeCaller. I saw in...
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Exome sequencing - additional public data for variant calling
Hi, I'm new to exome sequencing, sorry if the questions have really obvious answers. My data set contains only 3 different samples from mother, father and daughter. So far I'm doing the standard thing...
View ArticleVariant with great support not called.
This SNP has 30 reads supporting it with most of them being mapq60 and good fred scores. using version 3.4-46-gbc02625 and my command was java -jar ~/GenomeAnalysisTK.jar -R...
View ArticleWhy is HaplotypeCaller dropping half of my reads?
Hi I have been trying HaplotypeCaller to find SNPs and INDELS in viral read data (haploid) but am finding that it throws away around half of my reads and I don't understand why. A small proportion (8%)...
View ArticleCaller input_prior option
I'm using HaplotypeCaller (but it could be also possible to use this option with UnifiedGenotyper) for a very special experimental design in a no-human species, where we have an expectation for the...
View ArticleConfused by overlapping indels
Hi all, I'm currently confused about the snips called as shown below. If I am not mistaken, the first row shows gatk called an 34 bp insertion in sample 001 at position 3229753. It didn't call anything...
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