Why a true variant is not getting called by Haplotypecaller.
I am using HaplotypeCaller for calling the variants for 120 gene based target sequence. For gene PMS2, there is a variant with coverage 21 (in that position) Allele fraction of the alternate allele is...
View ArticleCalling whole-genome haplotypes for Chloroplast-captured Pooled Samples
I'm trying to call whole-chloroplast genome haplotypes for a pooled chloroplast-captured DNA sample from a non-model organism (no well-established variants). The reads are Illumina 100 bp PE reads, and...
View ArticleHaplotypeCaller and reads mapped to multiple locations
Dear GATK team, I've been trying to use GATK to call SNPs from RNA-Seq data mapped to a transcriptome assembly. I used Bowtie2 for the read mapping. I apologize if the information is already posted,...
View Articlemissing SNPs after gvcf combine and slow combination step
Hi, I'm using GATK ver 3.4 for SNP calling and I have some question about it. My data set has 500 samples, and I used genome data as reference for bowtie/GATK 1) I called SNP by sample (gvcf) with...
View ArticleI get very different MQ values when using GVCF vs BP_RESOLUTION
Hello! I had a question about the difference between using HaplotypeCaller's --emitRefConfidence GVCF vs BP_RESOLUTION. Maybe the answer is obvious or in the forum somewhere already but I couldn't spot...
View ArticleIn term of algorithms, what is the difference between haplotypecaller and...
Under every poster of GATK asking which is better, HC or UG, Geraldine always said HC. So Is there any documents talking about the detail algorithms HC and UG are using, so that I can get a clear idea...
View ArticleMonitor Progress of Haplotype Caller
Hello, we have a GATK automatic pipeline all set up. We noticed a run that looked finished but then noticed that some SNP/InDel calls were missing. We were able to see that Haplotype Caller died...
View ArticleHaplotypeCaller on whole genome or chromosome by chromosome: different results
Hi, I'm working on targeted resequencing data and I'm doing a multi-sample variant calling with the HaplotypeCaller. First, I tried to call the variants in all the targeted regions by doing the calling...
View ArticleEMIT_ALL_SITES in HaplotypeCaller
If I run HaplotypeCaller with a VCF file as the intervals file, -stand_emit_conf 0, and -out_mode EMIT_ALL_SITES, should I get back an output VCF with all the sites from the input VCF, whether or not...
View ArticleCan I apply the germline variant joint calling workflow to my RNAseq data?
We have not yet validated the joint genotyping methods (HaplotypeCaller in -ERC GVCF mode per-sample then GenotypeGVCFs per-cohort) on RNAseq data. Our standard recommendation is to process RNAseq...
View ArticleDisable AVX for pairHMM
Hi, I want to switch back to Java LOGLESS_CACHING implementation for PairHMM instead of AVX, how can I make this? I think that I may need to change some argument but I don't know where to start....
View ArticleCounting number of reads affected by N's in CGIAR
Hi, I work on plant species. I am using GATK on variant discovery in RNAseq data. I am not able to decide whether I should use option --filter_reads_with_N_cigar or -U ALLOW_N_CIGAR_READS. What do you...
View ArticleMemory heap size problem with Haplotype caller
Hello, I am trying to run HaplotypeCaller on my processed bam file but it keeps running out of memory. I have tried increasing the heap size to 90G but it still crash. This might have to do with the...
View ArticleBug in HaplotypeCaller?
I was just running haplotype caller on a pool, and it gave an error message which (if I understand the options I gave it correctly) should not occur. My command was: nice -n 5 java -jar...
View ArticleHaplotypeCaller says dict does not exist, but it does!
Hi All, I am running HaplotypeCaller and getting the error: ERROR MESSAGE: Fasta dict file...
View Articleparallelizing HC on PBS with Queue
Hi!!! I'm attempting to use Queue on PBSPro HPC cluster. I have tested the functionality of a custom scala script for Haplotype Caller and it is runnable. However, following the discussion on GATK...
View Articlevcf file generated using HaplotypeCaller does not contain dat lines
Hi, I typed the following command for finding snps and indels: java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R chr21/chr21.fa -I chr21/alignments/human38chr21.sorted.bam -o...
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 ArticleKeep "species" info from BAM to VCF
Hello, I am using HaplotypeCaller (GATK v3.5) with an input BAM file which has a header line like this (just a fake example): @SQ SN:chr1 LN:100000 SP:Arabis thal AS:2 M5:8668a646eada2f4...
View ArticleERROR:The requested extended must fully contain the requested span
I got this error when running HaplotypeCaller: ERROR MESSAGE: The requested extended must fully contain the requested span My command is: java -Xmx4g -jar ~/GATK_3.2/GenomeAnalysisTK.jar -T...
View Article