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CombineVariants in GATK4
Is it planned to add CombineVariants tool into GATK4.0 toolkit (it existed in previous GATK versions)? The only similar tool currently available in GATK4.0 Beta is GatherVCFs which has very limited...
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ALT * no deletion
Hi： my vcf, there is a "*", but I can't find the deletion in OF2-M bam by IGV 。I can't understand why ? GATK is 3.7 version。Haplotyper --emit_mode gvcf + GVCFtyper genome is not human. Thank you！ CHROM...
View Articleselect intersection, merged VCF files
Hi, I am using GATK3 and trying to compare two samples. I have a merged vcf file of two samples. I tried running below protocol. java -jar GenomeAnalysisTK.jar -T SelectVariants -R hg19.fasta -V...
View ArticleHow to get exact allele frequency using HaplotypeCaller-GATK4 and speed up...
Hi there, I have performed HaplotypeCaller in GATK4 (version:4.0.9.0) for variant calling of germline DNA. Here are the results in the vcf file. chr1 17365 rs369606208 C G 146.77 ....
View ArticleMeaning of --min_base_quality_score
What is the --min_base_quality_score mean ? Is it base on the mapping quality in the sam/bam file or the sequencing base quality? I'm a little bit confused by the description of the tool document in...
View ArticleMutect2 output vcf file is not giving any QUAL scores
Hi team GATK, Greetings from India! I am running GATK4 for somatic variant calling gatk Mutect2 -R ../../11_reference_genome/ref_gen_chr1_22_X_Y_final.fa --tumor-sample 01T -I 01T_sorted.bam -I...
View ArticleMutect2 bamout depths not matching vcf.
Hi, After running Mutect2 on tumor/normal paired bam files, I get an output VCF with unusually high depth counts. I understand that the numbers here can differ from the input bam depths due to genotype...
View ArticleSome questions on QD
Hello GATK team, I want to apply this to some GATK processed data I obtained from a reliable source. I noticed that the QD values (in my data) do not match the procedure explained here. Some questions...
View ArticleVariantRecalibrator - Can't do comparison because Locatables' contigs not...
Hi, sorry if the question isn't precise enough. Here's the command: tools/gatk-4.0.11.0/gatk VariantRecalibrator -R data/humanRefGenome/hs37d5.fa \ --variant...
View ArticleExtracting de novo mutation from multi sample vcf
Hi all, I'm currently trying to extract de novo mutations from my multi-sample vcf files (trios). I've already read the VCF file specification documentation but wanted to check if I got this right. So...
View ArticleInfuence of Coverage Depth Difference in Tumor & Normal Sequencing Data in...
Hi, GATK team. I'm planing to use Mutect & Mutect2 to call somatic mutations in Tumor and mathched Normal samples. I have a question about the coverage depth difference of Tumor and Normal samples....
View Articlevcf invalid GT allele index
Hi GATK team, I tried to subset vcf file using SelectVariants, but I got the error: The following invalid GT allele index was encountered in the file: "0. The subsetted vcf has only header lines and...
View ArticleGenerating a vcf with the information of specific genome positions (hotspots)
Hello, I'm developing a pipeline that needs to take into account the information about variants that are present on a list of hotspots on the genome, because my final analysis uses the information...
View ArticleMerging population vcf files without gvcf
Hi Everyone, I have two separate raw VCFs dataset processed by GATK version 3.5 (one from the population of ~ 2600 and one from the population of ~160). Since the upstream data cleaning and processing...
View ArticleHaplotypeCaller Incompatible Contigs DNASeq
I'm using GATK 4.0.11 and I'm getting the following error message when I run HaplotypeCaller on DNAseq data: 10:19:17.089 INFO HaplotypeCaller -...
View ArticleMutect on mm10
Hello, I am trying to run mutect on mouse, and getting the following error ERROR MESSAGE: Unable to parse header with error: Your input file has a malformed header: VCFv4.2 is not a supported version,...
View ArticleAnalysis Pipeline Discrepancy in SNP Calling and Coverage
Hi, All, So I am new to GATK so please bear with me... Essentially, I have developed a unix script to analyze the fastq sequencing output for a novel targeting technique. I am only targeting 27 SNPs...
View Articleformat fields and sample entries in VCF files
I've noticed a small bug with GATK tools and VCF files. CombineVariants and GenotypeGVCF can generate files where some samples have fewer fields than the format column. For instance, this is part of a...
View ArticleRemoving "chr" from CHROM field
Hello! I intend to use a training resource VCF that contains "chr" in the CHR field (Reference obtained from UCSC), which is incompatible with my raw call set (reference obtained from ensembl). I check...
View ArticleSelectVariants Starts Traversal but Does not Progress, High CPU Usage
Hi, I am using the GATK tool SelectVariants to only select variants that have passed FilterMutectCalls. Both FilterMutectCalls and Mutect2 were run in multi-sample mode, so the VCF being input to...
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