WARN messages with Haplotype Caller
Hi, I began a run using the --emitRefConfidence GVCF command asking for a .g.vcf file to be output for a single sample. Which is running (yay)! So far, it is still running and has thrown up several...
View ArticleClik here to view.
Using GATK: create a F0 SNP library and then genotype F2 sample using it
Hello GATK community, I would like your comments/suggestions for my strategy. I have F0 samples with two different phenotype. I have F2 samples with unknown phenotype. I would like to create a library...
View ArticleHC Tag
Hello, I'm looking at the HC tag that comes out of the --bamOutput option in HaplotypeCaller in the corresponding bam file that is produced. I've noticed that some real reads (i.e. ones not labeled as...
View ArticleSeveral Annotations not working in GATK Haplotype Caller
I am using Genotype Given Allele with Haplotype Caller I am trying to explicitely request all annotations that the documentation says are compatible with the Haplotype caller (and that make sense for a...
View ArticleClik here to view.
Does GATK HaplotypeCaller has resume analysis feature
Hello there, I am calling variants on 800 exome samples using Haplotypercaller for some reasons the caller stopped the analysis on certain location on chromosome 5 (after 5 weeks and i have 10 weeks to...
View ArticleGATK3.8 vs GATK4 HaplotypeCaller
Hello, maybe I'm asking a naive question and maybe it has been answered somewhere else, but as the title states are there differences in the algorithm of the HaplotypeCaller between GATK3.8 release and...
View ArticleBest strategy to "fix" the Haplotype Caller - GenotypeGVCF "missing DP field"...
Hi, I've run into the (already reported http://gatkforums.broadinstitute.org/dsde/discussion/5598/missing-depth-dp-after-haplotypecaller ) bug of the missing DP format field in my callings. I've run...
View ArticleIn which step exactly the allele depth / frequency is used during variant...
I was thinking of how allele depth / frequency affect variant calling. I know that the HC is using Bayes to call variant. The question is how is allele depth / frequency information used during the...
View ArticleMemory error when using scatter-gather (haplotypecaller + GenotypeGVCFs) on...
Dear GATK team, I have prepared 100 WES processed BAMs and try to call variants and output them in a single VCF. I used scatter-gather WDL scripts following...
View ArticleConfusion in using gVCF mode
Hi I have problem in using HaplotypeCaller gVCF mode ( GATK4 best practices). Please let me know following problems: 1- Should we run gVCF even when we have one WES sample? 2- I have 3 WES samples,...
View ArticleHaplotype Caller ERC BP Res with nonref bases explicitly detailed
Hi GATK Team! I was wondering if there is a way to get Haplotype Caller in ERC BP Resolution mode to emit details for every base for every position? That is, for each position rather than just emitting...
View ArticleHaplotypeCaller haploid GVCF format error?
Hi all, I prepared a clean Bam file following GATK Best Practice and used GATK4 HaplotypeCaller to create a gvcf with ploidy1 option: gatk-4.0.2.1/gatk HaplotypeCaller --native-pair-hmm-threads 24 -I...
View ArticleGATK4beta6 annotation incompatibility between HaplotypeCaller and...
Happy New Year! I'm attempting to joint genotype ~1000 exomes using GATK4. I've run HC per sample with the following command: java -Xmx7g -jar gatk-package-4.beta.6-local.jar HaplotypeCaller -ERC GVCF...
View ArticleHaplotypeCaller crash expected haplotypes.size() >= eventsAtThisLoc.size() + 1
I'm running HaplotypeCaller (GATK 4) with --alleles argument and it is crashing on a particular --alleles VCF file record with a stack trace with error "expected haplotypes.size() >=...
View ArticleGenotypeGVCFs Estimated Runtime 5.9 YEARS!!!
Hello, I have 3 de novo transcriptomes for which I am trying to genotype all SNPs. Originally, I asked a question about whether the joint genotyping pipeline will correctly identify SNPs fixed in one...
View ArticleHaplotypeCaller Error: SAM/BAM/CRAM Invalid GZIP header
This is my GATK (3.5-0-g36282e4) arguments Program Args: -T HaplotypeCaller -R human_g1k_v37.22.fasta -nct 16 -I ref.22.500x.bwamem.sorted.bqsr.bam -I somatic_sim_af20_500x.bwamem.bqsr.bam -I...
View ArticleHaplotypeCaller crash with long allele in --alleles VCF
I am running HaplotypeCaller with the --alleles option and it is crashing. I've traced it to a very long line in the --alleles VCF file, with a very long allele. The line is: chr4 1394536 ....
View ArticleDoes Haplotypecaller assign genotype for each allele separately?
Hi, I read how haplotypecaller assign genotype in the following link, it says that for each position haplotypecaller will calculate the best genotype, so I wonder, if the positions are close, then will...
View ArticleDoes GenotypeGVCFs call SNPs fixed in only 1 sample?
Apologies if this was addressed elsewhere, but I have looked carefully through the documentation. Simply put: using the joint analysis pipeline of GATK's HaplotypeCaller (-ERC GVCF) ->...
View ArticleGATK 3.8: Allele-specific Annotations
I am using GATK-3.8.1 for HaplotypeCaller (using gVCF mode and then GenotypeGVCF) and I noticed that final VCF output from GenotypeGVCF has missing DP values. I found a workaround that while doing gVCF...
View Article