HaplotyeCaller - non-variant block records in gVCF
Hi, I have generated a gVCF for an exome (with non-variant block records) from a BAM file belonging to the 1000Genomes data. I am using GATK tools version 3.5-0-g36282e4 and I have run the...
View Articlesanger confirmed SNV present with HaplotypeCaller 2.7, absent with...
We performed variant calling on a whole-exome sequenced human internal control sample. We have a set of 60 confirmed Sanger sequencing SNVs for this sample, which are all detected when we use...
View ArticleHaplotypeCaller runtime error with --emitRefConfidence GVCF
I am trying to run the HaplotypeCaller on a bam file with multiple samples. It runs successfully without the ERC GVCF option, e.g. java -jar /home/unix/csmillie/bin/GenomeAnalysisTK.jar -T...
View ArticleCall Varients from RNA-seq for RNA editing detection
Dear GATK staff I would like to use the GATK tool for the detection of possible RNA editing events. I followed the RNA-seq best practice up to the variant calling step itself. There I hesitate to use...
View ArticlePolling different tissues and individuals
Dear GATK team, We want to run RNAseq SNP analysis on Arabidopsis. Can we build each pool from 6 different plants ( genetically similar individuals ), only 3 will be taken from leaves and 3 will be...
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Incorrect Heterzygous Calls
Hello! I'm pretty new to this so pardon me if this is formatted incorrectly or I'm missing something obvious. It looks like I have the same problem as:...
View Article99.76% of reads failing DuplicateReadFilter for targetome analysis
Hi, I am using GATK HC to identify variants in a target region of about 23kb with very deep sequencing. I get this message during HC that 99.76% of reads failing DuplicateReadFilter. This means that a...
View ArticleCalling variants in a small target region
Hi, This may not directly relate to how GATK works, but I am still asking to get your expert input (I do use GATK for this pipeline). I am trying to test my variant calling pipeline that I have...
View Articlewarning when running HaplotypeCaller
Hi everyone, I got the following warning when running the HaplotypeCaller. BAM index file M11.bai is older than BAM M11.bam Although the warning presents in the log, it also gives me a gvcf. Does this...
View ArticleBaseQRankSum variations with interval size in HaplotypeCaller
Analyzing the same sample with and without queue, I noticed a variant being filtered out in one of the runs with VQSRTrancheSNP99.00to99.90 in the filter column. In my debugging of the problem, I...
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 Articleinterval lists and -nct threading
Regarding the observation elsewhere: "HaplotypeCaller is slower when restricted to intervals": My test-bed is a 48 core, 100GB RAM CentOS 7 system with GenomeAnalysisTK-3.5 on it. If i submit the...
View ArticlePercent of variant reads to make a heterozygous call
Hi, I was wondering what is the min percent of variant reads GATK uses by default to make a heterozygous call and how to change this value if need be. Thanks!
View ArticleVCF output format problem when -ERC BP_RESOLUTION is used
In a discussion about using ERC, you provide some example VCF output lines like: 20 10000442 . T <NON_REF> . . . GT:AD:CD:DP:GQ:PL 0/0:56,0:56:56:99:0,168,2095 20 10000443 . A <NON_REF> . ....
View ArticleWhich is the best tool for Variant calling of a non-model organism (Non-tumour)?
Hi All. I have been using #Haplotyplecaller for SNP calling for my organism of study. Recently, I came across #MUTECHT2 tool by GATK which states that it works better for calling spmatic mutations. But...
View ArticleBase recalibration and variant calling(with joint genotyping) for a non-model...
Hi, In case we do not have a database of known sites for a non model organism, what is the best strategy to do the base recalibration and variant calling with joint genotyping when we have several...
View ArticleGenotypeGVCFs "VCF is malformed" error message
Hi, I've tried my best to find the problem but without luck, so my first post... First the background: I have used HaplotypeCaller to make GVCFs per individual for 2 cohorts of 270 and 300 individuals...
View Articlevcf / GVCF result sets differ
Hello, It seems that running HaplotypeCaller with -ERC GVCF and then running GenotypeGVCFs -stand_call_conf 30 -stand_emit_conf 30 gives a different vcf than HaplotypeCaller -stand_call_conf 30...
View ArticleMissing QD tags at some positions
Hey there, How can it be possible that some of my snps or indels calls miss the QD tag? I'm doing the recommended workflow and I've tested if for both RNAseq (hard filters complains, that's how I saw...
View ArticleUsing GATK haplotype caller and SHAPEIT genotype likelihoods
Dear all, I have a question regarding the use of the SHAPEIT genotype calling by consecutive use of GATK, BEAGLE, and SHAPEIT. I have used the GATK haplotype caller, giving rise to an output of .vcf...
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