Single-Cell population join calling
Hello folks, I have a question regarding the pipeline I should use to do some QC on my different samples of single-cell sequencing I have. Here's mainly the design of our experiment. We have different...
View ArticleMerging Genome VCF's for the Same individual
Hi this is pretty much a feature request for something I think would be useful, I mentioned it briefly at the Brussels workshop and it seems like it might be possible. In a couple of projects I'm...
View ArticleGATK 3.0 HaplotypeCaller RUNTIME ERROR
Hi, I am running Haplotypecaller for ~600 bams to perform gVCF call on a cluster (SGE qsub system). Each node has 32 cores, 256 GB RAM. I am running 8 tasks pernode, so each task has 4 cores and 32GB...
View Article"ERROR MESSAGE: Rod span 1:1-249250621 isn't contained..." while running the...
When I try to run the HaplotypeCaller I get this error below. Although I have searched the forum and elsewhere for solutions, I cannot solve the issue. I get "No Errors found" when I run picard.jar...
View Articlerules for max_alternate_alleles in HaplotypeCaller
Hi, I can't come to any clear conclusion how this parameter works. Help me, please. I worked on the same files with exact command but the max_alternate_alleles. In first command I put 1 for its...
View ArticleAlternate Alleles in VCF are more than 1 base
Hi there, I've removed INDELS from a multi-sample vcf from HaplotypeCaller using SelectVariants. However, the ALT 'SNPs' are more than a single nucleotide substitution. Eg....
View ArticleHaplotype caller handling paired-end reads
Hi GATK team. I have some questions regarding on haplotype caller. I saw the forums and know that haplotypecaller does handle paired-end reads. But I can't find a parameter to claim that my data are...
View ArticleHaplotypeCaller generates diff results on different CPUs
I encountered an interesting problem: running HaplotypeCaller on different machines generates different result for 2 sites. The machines use the same input BAM file, same reference, same java...
View ArticleHaplotypeCaller - Genotype Given Allele Mode
Hi Team, I want to call variants for some samples using Genotype Given Allele mode(GGA) of HaplotypeCaller. I have used UnifiedGenotyper earlier in GGA mode. I am not sure about the right approach to...
View ArticleGATK RUNTIME ERROR (version 3.6-0-g89b7209) running HaplotypeCaller single...
Hi, Following "best practice", I am running haplotypecaller for each individual with the command java -Xmx131072m -jar GenomeAnalysisTK.jar \ -T HaplotypeCaller \ -I bam \ -o g.vcf \ -R...
View ArticleAny way to restrict HaplotypeCaller to work only on a set of regions?
Hi, for diagnostic purposes, I would like to run HaplotypeCaller on very small regions (even just a single base locus). I thought that was what the -AR switch was for, so I have: java -jar...
View ArticleGet all VCF files in proper format?
Hi, I tried running the following command to generate the VCF file using Haplotype Caller java -jar GenomeAnalysisTK.jar -T HaplotypeCaller --dbsnp chr7.vcf -R chr7.fa -I chr7.bam -A AlleleBalance...
View ArticleA question about using GenomeAnalysisTK to deal with ancient DNA data
Hi,Team, I want to call variants for some ancient samples using HaplotypeCaller. My command is as follows: java -jar GenomeAnalysisTK.jar -R myref.fa -T HaplotypeCaller -ERC BP_RESOLUTION -I 1.bam -L...
View Articlejava.util.NoSuchElementException exception in HaplotypeCaller
One out of my 200 samples failed, no matter using single thread more multiple threads. Here is the message: INFO 15:27:03,632 ProgressMeter - 1:148025863 8.6339635E7 3.5 m 2.0 s 5.7% 61.9 m 58.4 m INFO...
View ArticleStoring HC phased PGT into GT
Dear team, I am very excited to be able to use phased genotypes for various genetic analyses. Based on GATK best practices, I have generated a VCF using HC/GenotypeGVCF. I noticed phased genotypes were...
View ArticleHaplotypeCaller non-descript error
Hello all, I'm trying to run HaplotypeCaller on a bam that I've created following the Best Practices, however it fails and gives me the following error message: ERROR...
View ArticleDifferent ARO with or without -justDetermineActiveRegions for HaplotypeCaller
I noticed that for one BAM, when calling HaplotypeCaller (I am using version 3.5), with or without the -justDetermineActiveRegions, the ARO results are different at several intervals. For example, one...
View ArticleI do not get the annotations I specified with -A
The problem You specified -A <some annotation> in a command line invoking one of the annotation-capable tools (HaplotypeCaller, MuTect2, UnifiedGenotyper and VariantAnnotator), but that...
View ArticleAre there published guidelines for interpreting FS (FisherStrand) and SOR...
I have recently come across some false positive variant calls, for which visual inspection revealed obvious strand bias. I looked at the FS and SOR scores for these variants but they do not seem to...
View ArticleReference genotype quality in presence of conflicting reads
Given the following line from a VCF file: Supercontig_1.1 308 . T A . PASS...
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