Error in VariantAnnotator
hi Because my reference is in scaffold level and GATK not designed to analyse such referenes, thus my variant caller project done using samtools. Now i want to add QD(qualityofdepth) to vcf files using...
View ArticleAlignment and Variant calling using hg38DH
Dear GATK Team, I want to perform alignment and variant analysis for whole genome sample using hg38DH build. I have gone through forum and came to know that it is quite different. here is the reference...
View ArticleCombineVariants error unexpected bases in allele bases '*T'
Hi there, I ran the following command java -jar $gatk_jar -T CombineVariants -R ${hs37d5} \ --variant ${name1} --variant ${name2} \ -o combined.vcf \ -genotypeMergeOptions UNIQUIFY I followed the best...
View Articlepicard.sam.MergeBamAlignment fails
Hello, I'm a new user to Picard. I am running Picard as part of a pipeline in Drop-Seq. My command is [Thu Nov 24 08:22:35 EST 2016] picard.sam.MergeBamAlignment...
View ArticleHow to fix "mis-encoded base qualities"? Is there a recommended program?
GATK BaseRecalibrator and UnifiedGenotyper gave the same error messages as below. Basically, gatk doesn't take my bam file because of "mis-encoded base qualities". What can I do with the base...
View ArticleFastaAlternateReferenceMaker not replacing bases at all variant sites in the...
Hi, I have processed a Canine Whole Exome sequencing data set using GATK and generated a VCF file with variants. My end goal is to get the DNA sequences corresponding to each variant with the reference...
View ArticleUnmappedReadFilter
I would like to know how UnmappedReadFilter identify umapped reads from bam files? one more thing, the read count is much higher than number of reads i have in the original sam file.So, how mutect2...
View ArticleUnified Genoptyper joint calling on poolseq data: variable ploidy
Hi, I know Unified Genotyper has been superseded by Haplotype Caller, though due to time constraints (and other) I am committed to use UG. I have 14 population pools with variable numbers of...
View Articleerror: use BaseRecalibrator do BQSR
I try to use BaseRecalibrator to generate a .grp file or a .table file, so I could do variant call after that my input file is bam file which has been sort/add header/Duplicates Marking/index/Local...
View ArticleMergeBamAlignment Failure
Hello, I'm trying to use Picard 2.9.0-1-gf5b9f50-SNAPSHOT's MergeBamAlignment, but get this error: this command: java -jar ../picard.jar MergeBamAlignment...
View ArticleHaplotypeCaller v3.7.0 alternative allele depth not emitted
Hi I just noticed the alternative allele read depth is missing for a true positive insertion called with HaplotypeCaller v3.7.0. #SNPs and Indels GVCF with Haplotypecaller...
View ArticleBimodal MQ distribution
Hi GATK-team, I am working with a dataset of WG human samples (Illumina paired-end, ~30X) comprising about 120 samples, all from Africa (from ~25 different populations). For 2/3 of the samples the data...
View Article[WDL][Cromwell] Submitting a workflow with a subworkflow to the cloud.
Hi, I am having an issue with how to appropriately submit a WDL workflow to the cloud when a subworkflow is involved, which I have not been able to find anything in the forums or spec sheets to explain...
View Article(howto) Call variants with HaplotypeCaller
Objective Call variants on a single genome with the HaplotypeCaller, producing a raw (unfiltered) VCF. Caveat This is meant only for single-sample analysis. To analyze multiple samples, see the Best...
View ArticleCosmic variants vcf and picard SortVcf
Dear GATK team, I am using MuTect2 to call somatic mutations from normal and tumour paired sample.One of the parameter is --cosmic I downloaded Cosmic VCF file from sftp-cancer.sanger.ac.uk,...
View ArticleIndelRealigner runtime error with GATK version 3.5-0-g36282e4
Hi, I was trying to map a WGS sequence following the GATK best practice. I used bwa -mem to map. Then I used picard to sort, mark duplicates before passing into the IndelRealigner. When running the...
View ArticleVQSR: Negative Number of SNPs in tranche
Dear GATK-Team, using VQSR on pig pooled data prepared according to the best practices pipeline, I encounter negative numbers of SNPs in the tranch plot. Following your recommendations for species with...
View ArticleRuntime Error, SRA Accession problem.
Hello. My DepthOfCoverage returns RUNTIME ERROR, which is strange, because exactly the same command worked perfectly yesterday. Seems like I'm having a problem with automatic downloading of SRA toolkit...
View ArticleFalse indel PASSed but not covered in IGV
Hi there, I came across a set of false positive indels obtained in some targeted sequencing experiments. Situations are similar to the following, where a deletion looks to have high quality, according...
View ArticleWhy analyze RNAseq samples together to boost the variant discovery ?
Hi, I'm working with RNAseq data from one patient (2 conditions), you recommend analyzing all samples together, because it will boost the discovery power, why ? Many thanx, Jennifer
View Article