What is the difference between SplitVcfs (Picard) and SelectVariants?
Hi all, Usually I do splitting SNPs and INDELs from VCF file using "gatk SelectVariants" for SNPs --select-type-to-include SNP and Indels --select-type-to-include INDEL. Accidentally I came to see the...
View ArticleError: Input files reference and features have incompatible cont; while...
Hi All, While I am running SelectVariants modules for splitting SNPs ans Indels from 1000GP phase3 vcf files, it throws an error "A USER ERROR has occurred: Input files reference and features have...
View ArticleHow do I get the unique SNPs for each strain?
Hi, First, I would like to say that I'm new to genome and variant calling data analyses and, of course, to GATK. I read some tutorials and the BestPractices guide before I start. I'm using gatk version...
View ArticleWhat variants does Mutect2 --germline-resource filter out?
Hi everybody, I am new analyzing WES and I try GATK4 workflow for the detection of somatic variants. I run Mutect2 in tumor-only mode with these commands: gatk Mutect2 -R reference.ucsc.hg19.fasta -L...
View ArticleHow to select samples that are polymorphic on a specific locus from a joint...
Hi, I am trying to select the samples that are polymorphic on a specific locus from a joint genotyped vcf file using SelectVariants tool and JEXL expressions with no success. The command I am trying to...
View ArticleVariantFiltration not filtering 'NA' QD values when filtering QD
I am running VariantFiltration with "--filter-expression "QD < 2.0" I then run SelectVariants with "--exclude-filtered". In the output file, all SNPs with a numeric QD value of < 2.0 are indeed...
View ArticleUsing GATK SelectVariants to filter based on calculated allele frequency
Many of the variant callers I use, such as Pindel, do not include the AF or allele frequency value in the vcf output. However I still need to filter the vcf based on the allele frequencies of the Tumor...
View ArticleCreating updated resources from gnomAD for somatic variant calling (Mutect2)
Hi, I want to call somatic variants in tumor-only mode with Mutect2. For the GRCh38 reference, in the GATK Resource Bundle I found the files af-only-gnomad.hg38.vcf.gz (to remove germline muations) and...
View ArticleGATK3.8 SNP near the INDEL region with something different
Hi, I filter the SNP by using GATK3.8. When I check the SNP manually, I found this site with AD 15,0 and GT 0/1. I'm not sure about this result. Is it wrong ? or could I change the GT manually? Thanks...
View ArticleTrio or SelectVariants
I have 25 samples of exome sequencing data from 6 families on normal and diseased individuals. Two are joint families with data available for affected/unaffected uncles and aunts. I am not sure if I...
View ArticleSelectVariants - java.lang.IllegalStateException: Allele in genotype not in...
Hi everyone, I'm trying to select variants with SelectVariants but for some reason it stops saying that Allele in genotype CT* not in the variant context [CT*, C]. I tryied to find a CT* in the VCF...
View ArticleSelect Variants only keeps INDELs
Hi, I have successfully used Select Variants before to subset a large VCF into a smaller VCF that contains only certain IDs and variables. Now, using the exact same code and variables I am finding that...
View ArticleSelectVariants produce empty files
I have 8 samples of genome sequencing data with a different condition. The question is to identify variants for each sample. I followed best practice GATK for variant calling...
View ArticleFilter coding germline variants from 100 human WGS gVCFs
Hi there, My aim is to filter germline coding variants from 100 human WGS gVCFs. I was wondering what would be the best approach. I am using GATK Best Practices (version 4.1.0.0) on two local servers....
View ArticleSuggestions on how to correct this malformed vcf
Hello! Trying to filter a variant call set using SelectVariants, I get the followin error: htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 141: 0 is an...
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 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 ArticleLoss of RSIDs for GenotypeGVCFs, possibly an issue with dpsnp filter.vcf file...
Hello, I've run into this problem a few times now having attempted to debug the issue in various ways. The first time it occurred I was using a vcf file containing the rsids I wished to genotype on a...
View ArticleTrimming a GVCF with "-L"
GATK team, I currently have many WES gVCFs called with GATK 3.x HaplotypeCaller, and I'm now looking to combine them and run GenotypeGVCFs. Unfortunately, I forgot to add the "-L" argument to HC to...
View ArticleSelectVariants
Hi, I have used VariantFiltration to filter the variants based on quality thresholds. Subsequently, SelectVariants to select the filter passed variants using "--excludeFiltered" flag in the command...
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