% of mapped reads
What tool in Picard will tell me the number of reads that mapped to my reference sequences? I want to know the percentage of mapped reads, i.e. number of reads mapped/number of total reads
View Article[GATK 4.1.0.0] Funcotator issues.
Hi, I have questions in using Funcotator in GATK 4.1.0.0. My input vcf uses b37 (GRCh37) as a reference. 1) What are chr1_a_bed and chr1_b_bed in the resource bundle,...
View ArticleVariants estimated by gatk4 mutect2 are dramatically less compared estimated...
Dear GATK team. Hello. I'm GATK4 user. I compared the number of variants between gatk4 mutect2 raw variants and Vardict raw variants. As compared between output of callers, I identified they are so...
View ArticleGather task proceeded without awaiting input from scatter output
Dear all, I'm trying to incorporate the CNN filtering in my Germline variant discovery work flow but noted some abnormal behaviour of Cromwell. My scatter is followed by a gather task (MergeVCF_HC4)...
View Articlesplit multiallelic variants before VQSR and CNNScoreVariants, gatk team opinion
Hi, if I remember well I saw in the forum a user to suggest to split the multiallelic variants before VQSR. I think that is something logical (I never done before), but I would like to know the opinion...
View ArticleFuncotator log4j Error
I am running Funcotator on a full VCF resulting in an empty VCF. I think it is due to an error in the log4j system "No appenders could be found for logger". I have seen this issue reported by other...
View Article--dontUseSoftClippedBases option seems to involve non-softclipped bases
Hello, I am checking the differences between the calls with/without using soft clipped bases. Some of the missed calls when '--dontUseSoftClippedBases=true' (compared with the calls when 'false')...
View ArticleFilterMutectCalls error :"there is no such column: sample"
Hi, I've been following the best practice for tumor somatic mutation calling. Everything runs like a charm until FilterMutectCalls which keeps throwing a java error:...
View ArticleHow to find HaplotypeScore?
I was running haplotype score and got a warning message :Annotation will not be calculated, must be called from UnifiedGenotyper. Can you please tell the command to calculate Haplotype score using...
View ArticleCould I run ASEReadCounter on homozygous SNPs?
The documentation of ASEReadCounter states that this tool is designed for heterozygous SNPs. However, could I still use it to calculate ref and alt allele read depth on hom-SNPs? My purpose is to check...
View ArticleSelectVariants V4 TribbleException Contig chr1 does not have a length field
I indexed my VCF file with GATK V4.0.6.0 IndexFeatureFile, then ran GATK V4.0.6.0 SelectVariants on it, and I got an exception: htsjdk.tribble.TribbleException: Contig chr1 does not have a length...
View ArticleCombine gvcf files generated with GATK and Isaac
Hi. I have a batch of g.vcf files generated with IsaacVariantCaller. I also have another batch generated with GATK HaplotypeCaller. I want to combine these to batches to perform GenotypeGVCFs. Is there...
View ArticleError with FastaAlternateReferenceMaker
Hello, I am having some trouble running the FastaAlternateReferenceMaker tool to convert my vcf sequences to fasta using a reference genome. I started with a multi-sequence vcf made from whole genome...
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[GATK 4.0.0.0] joint calling for Mutect2?
Hello, I am interested in inferring clonal evolution using somatic variants called by Mutect2. One way to infer is by tracking VAF (variant allele fraction) of somatic variants in multiple time points...
View ArticleCNNScoreVariants Hanging in 4.1.0
I am trying to run CNNScoreVariants in GATK 4.1.0 but the tool seems to hang on the 'INFO NativeLibraryLoader - Loading libgkl_utils.so from jar' step for both the 1D and 2D models. My issues seems...
View Articlehow to do BQSR on WES or other targeted sequencing?
I have this question because of the following statement from this article: In addition, there are some processing steps, such as BQSR, that should be restricted to the capture targets in order to...
View ArticleGATK4.1.0.0's VariantRecalibrator resource format differs from GATK4.0.11.0?
Hi, When I used GATK4.1.0.0 to vqsr, I found it reported the error, but I tried the beta version GATK4.0.11.0, it ran well. And the input VCF file I used was produced by the old tool CombineGVCFs and...
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FastaAlternateReferenceMakers 4.1.0.0 doesn't give expected output
Hi GATK team, I run this line: ./gatk FastaAlternateReferenceMakers -R Galaxy47-[ARS-UCD1.2_Btau5.0.1Y.fa.gz].fasta -O Chr20a.SRR4296972.fasta -V Chr20.SRR4296972.g.vcf.gz But, the tool doesn't change...
View ArticleHow are supplementary alignments handled by HaplotypeCaller?
Hello, I am curious about how HaplotypeCallers deals with secondary alignments. I know (based on the documentation and my own runs) that the filter NotSecondaryAlignmentReadFilter is applied but I do...
View ArticleJava errors with GATK when running on rna-seq data in serial mode using GCC
Hi, I am using GATK 3.8. I had done some analysis with DNAseq data that went seamlessly but now I am working on calling variants using RNA-seq. I had run everything till the split-reads part but then I...
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