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Should I analyze my samples alone or together?
Together is (almost always) better than alone We recommend performing variant discovery in a way that enables joint analysis of multiple samples, as laid out in our Best Practices workflow. That...
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Reference Genome Components
Document is in BETA. It may be incomplete and/or inaccurate. Post suggestions to the Comments section. This document defines several components of a reference genome. We use the human GRCh38/hg38...
View Articlehard-masked analysis set of GRCh38
Hi, happy new year. It is said that in the analysis set of GRCh38, duplicate copies of centromeric and genomic repeat arrays (on chromosomes 5, 14, 19, 21, & 22) and two PAR regions on chromosome Y...
View Articlecalculating sigma for Depth of Coverage cutoffs
Hi, I would like to filter variants based on max DP. I understand that in order to define the max DP cutoof there is a need to calculate the Sigma, as stated in GATK's best practices: "The maximum DP...
View ArticleRemoving overlapping variants from one VCF file from another?
Hello! Firstly let me say the support in this forum is amazing and we are very lucky to have you guys listen and respond to our issues! I have illumina DNA sequening of bacterial populations which are...
View ArticleWhy the candidate like this is rejected? It seems to meet all requirements.
contig position context ref_allele alt_allele tumor_name normal_name score dbsnp_site covered power tumor_power normal_power total_pairs improper_pairs map_Q0_reads t_lod_fstar tumor_f...
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picard liftovervcf parsing error
I am using picard liftover vcf to algin variants from hg38 to hg19. I am not sure what the error is referring to though it seems to be an issue with the vcf (I have copied a few lines of the format)....
View ArticleERROR MESSAGE: For input string: "0.000" - Variantfiltration - GATK 3.7-0
Hi, I encountered an issue with the current version of GATK. I received the following error message : ERROR MESSAGE: For input string: "0.000", when I ran this command : 'java -Xmx2g -jar...
View ArticleHaplotypeCaller: False negatives near intron boundaries
Hi, I am running HaplotypeCaller on RNA-seq, following the best practices instructions at this page: https://software.broadinstitute.org/gatk/guide/article?id=3891 I am running the pipeline on NA12878,...
View ArticleQuality Score per sample
Dear Dev, I didn't find anything in your forum about my question. I'd like to know if you support an annotation, during variant calling on germline experiments, in FORMAT field, to report for each...
View ArticleSomething about Create PoN workflow
While running 'CreatePanelOfNormals' , some errors occured. Here is the code i ran 'java -Xmx16g -Djava.library.path=/Workspace/Software/HDFView/HDFView-2.13.0-Linux/HDFView/2.13.0/lib/ -jar...
View ArticleErro about Create PoN workflow
I used HDF-2.11 , but something wrong still occured. As following : [January 11, 2017 11:24:15 AM CST] org.broadinstitute.hellbender.tools.exome.CreatePanelOfNormals --input merge.1.txt --output...
View ArticleErro about Create PoN workflow
I used HDF-2.11 , but something wrong still occured. As following : [January 11, 2017 11:24:15 AM CST] org.broadinstitute.hellbender.tools.exome.CreatePanelOfNormals --input merge.1.txt --output...
View ArticleIncrease max allowed compute PLs for an allele
When running GenotypeGVCFs (v3.7), I get a small number of sites (<100) that are not called because of: DEBUG 13:35:31,518 ReferenceConfidenceVariantContextMerger - location chr21:44483184 has too...
View ArticleOncotator -- Variant classification and Secondary variant classification
There are 22 values for Variant classification, and 7 values for Secondary variant classification in Oncotator output. Can any one please tell me what the values mean? Also, can any one please tell me...
View ArticleCount of reads F1R2 and F2R1 annotations
Hello, From the Mutect2 output VCF, how does one interpret the values for the annotations of F1R2 and F2R1? In the example below for a given position in a VCF: chr5 32902979 A C...
View ArticleHaplotype caller reports a variant when using the gVCF format but not when...
Dear GATK team, I have a variant that is called when setting the --emitRefConfidence to GVCF but it is not called when the output is switched to the VCF format. gVCF output: chr11 108250864 . G C,...
View ArticleHaplotypeCaller not catching variants
Hello, I am currently having an issue where HaplotypeCaller is not catching at least one specific variant. I have searched forums and have used the -bamout option as suggested by some. While the bam...
View ArticleHow to explain the CNV result produced by GAKT4
I've got the CNV result produced by GATK4, but I can't understand it. As you see, the value of 'Segment_Mean' in the second line nearly equal to which in the third line, but why the result of...
View Articlepossible bug in GATK3.7
Hello, I started the variant filtration step with GATK 3.7 (see attached file and got immediately an error message). I switched to the version 3.6 and used the exact command line and it worked. So...
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