How can i use the optional tool; OUTPUT_VCF?
Dear, How can i use the optional tool; OUTPUT_VCF? I saw https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.5.0/picard_vcf_GenotypeConcordance.php. I entered below command. However, i...
View ArticleDisable duplicate read filter for M2
I have high coverage targeted sequencing data and would like to disable the duplicate read filter for Mutect2 (rather than skipping the de-duplication step in alignment). Do I understand the...
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GATK4 GetPileupSummaries
Hi, I use GATK GetPileupSummaries to estimate contamination, the output has many sites, as in the following picture so, which sites are used to estimate contamination? can someone point these sites in...
View ArticleMutect2 "--mitochondria" flag doesn't work
First of all, since this is my first question on the forum, I wanted to thank you for all the help so far and the help that I will definitely get in the future. Now to the actual question: I am working...
View ArticleDoes GATK4 v4.1.1.0 support MarkDuplicates?
I've run GATK3.5 with `MarkDuplicates`, but can't get it to run with GATK4 v4.1.1.0. I double-checked the best practices for data pre-processing for variant discovery and noted that the command...
View ArticleIntervals that cross chromosomes
Hi team. I'm trying to put together an interval list (in any format that can be used by GenotypeGVCFs) that crosses chromosomes (multiple chromosomes within one interval). This is for most efficient...
View ArticleHow much memory should it require to run MergeVCFs on 2500 samples?
My MergeVCFs job is not outputting any logs on FireCloud, just sitting there for several days without finishing. We ran this sucessfully on 1200 samples with just 8 GB of RAM, so it's hard for me to...
View ArticleInstalling GATK4 via Conda
Hi there! I have a small problem, or a suggestion for improvement, related to the use of (Mini)conda and GATK4. I'm not entirely sure if this forum is a right place to ask this because I don't really...
View ArticleCould you please let me know any tool, to concatenate the gvcf files? Or...
Could you please let me know any tool, to concatenate the gvcf files? Or there is any other solution to run the intermediate HaplotypeCaller in GVCF mode on parts of the chromosome to speed up the...
View ArticleAnnotation problem: not all variants are taken into account
Hello, I use GATK version 4.1 to annotate a vcf with the following command : java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true...
View ArticlePotential for merging GenomeDBs or adding to an existing database
Hello, I have adopted using GenomicsDBImport for my workflows involving ~2500 samples to begin. This data structure works well and I am very happy it was implemented. However my data is such that I...
View ArticleGATK FastaAlternateReferenceMaker not correcting fasta reference
Hi, I am trying to use "GATK FastaAlternateReferenceMaker" but the output fasta file is the same as the one used in input. In other words, my fasta genome file is not corrected according to the vcf...
View ArticleVQSR extremely low numbers of TP variants in tranche.(0.01 novel...
Dear staff, (wondering why am only allowed to select "Zoo & Garden" for the category...HELP) I have 45108 variants from 31 exome vcf files. After VariantRecalibrator, my tranche specificity shows...
View ArticleIs DP the right criteria to be used in whole exome sequencing.
I have whole exome sequencing data from multiple mice. I have performed GATK4.1 pipeline and for recal i have used dbSNP142 and also snpeff. Can I consider DP=100 as the minimum value to filter the...
View ArticleHow MuTect filters candidate mutations
Please note that this article refers to the original standalone version of MuTect. A new version is now available within GATK (starting at GATK 3.5) under the name MuTect2. This new version is able to...
View ArticleGetting specific information from Mutect or Mutect2 output
Hi Long time I am seeking for which variant caller gives me read depth for tumour and matched normal also Number of variant bases at the position in the tumor sample from called SNVs and indels; I used...
View ArticleMissing metrics for a sample with CollectVariantCallingMetrics
Hi, I am using CollectVariantCallingMetrics on vcf generated with GATK, version 4.1.1.0 and my Picard version is 2.1.0. Interestingly while my vcf has 4 samples, I got the metrics for only 3 samples....
View ArticleMergeBAM RG ID and SM tags
Dear GATK team, I have gone through the discussion on Merging lane wise bam and still I have little confusion. Does it make difference if we have same RG ID and SM tags across all lanes as it was...
View ArticleGATK 4.1.0.0 Mutect2 error with gnomAD AF file
I'm running into an error when running GATK 4.1.0.0 with the following call: java -Xmx16g -jar ${gatkDir}/GATK.jar Mutect2 -R ${GRC}.fa -I ${TU}.recal.bam -tumor TU -I ${NM}.recal.bam -normal NM...
View ArticleQuestion about GATK4 SplitNCigarReads tool
Hi, I used the GATK SplitNCigarReads tools to process RNA-Seq data, which is said to reduce the false positive rate. Then, the processed data was used for SNP calling(by using variant calling tools in...
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