I need help. GATK Haplotypecaller says my dict is empty but it isn't??
The Error message I get is the following INFO 12:25:14,659 HelpFormatter - ---------------------------------------------------------------------------------- INFO 12:25:14,662 HelpFormatter - The...
View ArticlePhasing
Hi there How do u incorporate phasing with your variants if you dont have data from parents. my haplotype output is 1/1 not 1|1 so how can we say haplotyper can give phased haplotypes. Huma
View ArticleHaplotypeCaller pooled sequence problem
Hi, I have a number of samples that consist of multiple individuals from the same population pooled together, and have been truing to use HaplotypeCaller to call the variants. I have set the (ploidy to...
View ArticleWhat is the size of the internal window used by gatk haplotypecaller's...
Hello gatk community, Since gatk haplotypecaller is ran by a sliding window approach, the variant calling on each position seems to also depend on the presence/type/absence of variants on the flanking...
View ArticleOutput active regions in GATK4 HaplotypeCaller
Hi What would be the best way to output active regions from GATK4 HaplotypeCaller? In GATK 3.x, an option --activeRegionOut <file name> could be used to write active regions in a TSV file....
View ArticleHaplotypeCaller calling as heterozygotes incorrectly
I am finding that HaplotypeCaller is calling heterozygotes when there is no evidence when you look in IGV. Is this still a known problem? I am using version 2.8-1-g932cd3a. Attached are two screen...
View ArticleGATK HaplotypeCaller Error: Java stack error
I get the same error repetitively while running GATK HaplotypeCaller (see below). This seems to occur around the same chromosome positions for each of the 3 bam samples. Rest of the samples run without...
View ArticleAdvice ERROR ----------
I am using the workflow for best practices for variant calling. I used the sam files obtained with bowtie So far I index and create the .dict files using this commands: java -jar...
View ArticleSomatic mutations of epithelial cells (HaplotypeCaller vs Mutect)
Hello, I'd like to extract somatic mutations from normal epithelial cells of cancer patients. And it's confusing which tool to use. HaplotypeCaller or Mutect? I know Mutect is for calling somatic...
View ArticleWhat is the best practice for calling/combining variants across multiple...
Hi, I am working with RNA-Seq data from 6 different samples. Part of my research is to identify novel polymorphisms. I have generated a filtered vcf file for each sample. I would like to now combine...
View ArticleHaplotypecaller: Problem with using ploidy argument.
Dear GATK team, I tried to fix the ploidy issue with sex chromosome in my pipeline, based on the information that I got from the previously asked questions. However, when I run that, there is No...
View ArticleHaplotypeCaller what is j in calculation of genotype likelihood?
I have read the Methods and Algorithm section HC step 4: Assigning per-sample genotypes. I follow up until the equation for P(D|G) that includes a product over j. Please explain what j is. Are you...
View ArticleHaplotypeCaller - number of haplotypes/alleles to allow
If I am analysing a single sample, can I specify a lower value for maxNumHaplotypesInPopulation and maxAltAlleles? Should these variables scale with the size of your sample population?
View Articlewhat does the minReadsPerAlignmentStart argument in HaplotypeCaller mean?
The minReadsPerAlignmentStart argument in HaplotypeCaller is described as the minimum number of reads with the same alignment start for each location in an active region and has a default of 10. For...
View ArticleHaplotypeCaller with very low coverage/inconsistent coverage bam file
Hello, I recently had to download some SOLiD datasets (whole genome, non-human) from a paper published in 2010 and perform SNP calling using those reads. I roughly followed the best-practices...
View ArticleIs it possible to suppress the NON_REF tag on variant calls?
Hello, In GVCF output from HaplotypeCaller, each line contains the allele, including the lines with explicit variant calls. Is there a simple way to suppress the allele on variant calls? Also, what is...
View ArticleVersion highlights for GATK version 3.5
The last GATK 3.x release of the year 2015 has arrived! The major feature in GATK 3.5 is the eagerly awaited MuTect2 (beta version), which brings somatic SNP and Indel calling to GATK. This is just the...
View ArticleHaplotypeCaller in GVCF mode for trio
Hello! I am setting up a GATK pipeline for analysis of trio. I have run all the step perfectly up to HaplotypeCaller, then GenotypeGVCFs, and finally PhaseByTransmission walkers. However, by manually...
View ArticleRelationship between depth and genotype?
Hi, I am new to WGS and would like to know how the genotype is attributed. It seems it does not depend much on depth of allele ratio. We ran GATK3.6 and Freebayes on the same BAM 50-50X files and...
View ArticleIncorrect Likelihood / AD Count For Variant
I am trying to figure out why a site is being called with the wrong AD / Likelihood and what can be done about it. In particular, there is a site in my VCF that is being called with a very wonky AD...
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