Error: DP annotation : HaplotypeCaller in GATK pipeline
I was following the GATK pipeline for my patient data to find the germline mutation. I was okay until the BQSR procedure. ( the output file is patient1.sorted_dupl_realign_recalib.resort.bam) Then, I...
View ArticleWhy the option -env did not exclude all the non-variant sites ?
Hi, I use SelectVariants to remove some sample out of may initial data. In doing that, I ended up having some sites for which there is no variant as the variation was removed with samples that had been...
View ArticleHow to mark specific individual genotype as No Call
Hi, I have been trying to find a way to mark specific individual genotypes as No Call. I know that in VariantFiltration it is possible to add the option --setFilteredGTToNocall in order to mark...
View ArticleWhen does IndelRealigner discard reads?
I'm using IndelRealigner on version VN:3.4-46-gbc02625, command line field is: CL:knownAlleles=[]...
View ArticleHow can I invoke read filters and their arguments?
Most GATK tools apply several read filters by default. You can look up exactly what are the defaults for each tool in their respective Technical Documentation pages. But sometimes you want to specify...
View ArticleInterpreting Allele frequency equal to 1.0
Hi, In the following vcf file, the AF allele frequency of ALT allele is 1.0. Does it mean that it is not a true SNP of interest? Does it also mean that ALT allele always occurs and REF allele never...
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 ArticleMuTect2 high insertion counts?
Hi Folks I am using Mutect2 to analyze blood vs. FFPE tumor samples (breast cancer). I am getting (what I think are) unusually high insertion:SNV ratios - the ratio is between 2:1 and 3:1, thus high...
View ArticleUnifiedGenotyper error: Somehow the requested coordinate is not covered by...
Dear GATK Team, I am receiving the following error while running GATK 1.6. Unfortunately, for project consistency I cannot update to a more recent version of GATK and would at least wish to understand...
View ArticleBug report: DepthOfCoverage csv output
Hi GATK team. FYI: when using DepthOfCoverage 3.6.0 using the following arguments: -T DepthOfCoverage -R $(REF) --validation_strictness LENIENT -L:capture,BED in.bed -I in.al --outputFormat csv -o...
View ArticleAre there published guidelines for interpreting FS (FisherStrand) and SOR...
I have recently come across some false positive variant calls, for which visual inspection revealed obvious strand bias. I looked at the FS and SOR scores for these variants but they do not seem to...
View ArticleReference genotype quality in presence of conflicting reads
Given the following line from a VCF file: Supercontig_1.1 308 . T A . PASS...
View ArticleClik here to view.
Should I analyze my samples alone or together?
Together is (almost always) better than alone We recommend performing variant discovery in a way that enables joint analysis of multiple samples, as laid out in our Best Practices workflow. That...
View ArticleBug with version 3.6 and jexl
I recently tried to use a GaTK command I previously used with GaTK 3.5, and I'm getting a jexl error. I don't understand why. I've updated to java 1.8.0_77 java -Xmx${MEM} -jar...
View ArticleDream challenge PON
Hello, The Supplementary Data for the Dream challenge (http://www.nature.com/nmeth/journal/v12/n7/full/nmeth.3407.html) indicates that a panel of normals filter was used for the Broad's Mutect...
View ArticleRunning HaplotypeCaller in GENOTYPE_GIVEN_ALLELES mode with...
Hi Sheila and Geraldine When I run HaplotypeCaller (v3.3-0-g37228af) in GENOTYPE_GIVEN_ALLELES mode with --emitRefConfidence GVCF I get the error: Invalid command line: Argument ERC/gt_mode has a bad...
View Articleabout the resource bundle for hg38 : about the vcf files
Dear all, please could you let me know whether there is a quick fix for the VCF files in the bundle for hg38 (available at ftp://ftp.broadinstitute.org/bundle/hg38/hg38bundle/): particularly,...
View ArticleIs it possible to make VariantAnnotator check REF and ALT fields?
Hi! So we use GATK a lot in our research, it works amazingly well most of the time, so first of all, thanks for creating it! We have this one problem that we were unable to solve on our own. Say we...
View ArticleClik here to view.
Extremely high depth of coverage
Dear all, I've run the DepthOfCoverage tool on 263 WGS samples and have found some unusual total and averages for some regions. Does it mean any sort of error on the alignment or I can just filtered...
View Articleabout VQSR -- VariantRecalibrator
Dear all, please could you advise on the following : how is more appropriate to set up the VQSR as I have noted some discrepancies between different resource materials ? Here is what I mean : I. about...
View Article