Removing * Alleles
Hi, The program I am using for analysis considers * alleles inappropriate for analysis. From my understanding these are spanning deletions, but I am unsure how to properly remove them from my data. Do...
View ArticleHow to use --setFilteredGtToNocall and --maxNOCALLfraction with SelectVariants
Hello, I have a VCF file on which I first use VariantFiltration (GATK v3.7) with various filter expressions, such as "QD < 2.0" and "MQ < 40.0", as well as various genotype filter expressions,...
View ArticleGenotypeGVCFs AD=0
Hi! I have a sample for which HaplotypeCaller identifies the following variant: chr12 133237753 . GAAA G,GA,GAA,TAAA,GAAAA,GAAAAA,<NON_REF> 66.73 ....
View ArticleSelectVariants modifies VCF entries, keeping only the base calls intact.
I am using GATKv3.5. I used SelectVariants as shown below to remove 11 samples from a vcf file: java -jar GenomeAnalysisTK.jar -T SelectVariants -R reference.fasta -V all_samples.vcf -xl_sn sample90...
View ArticleSelectVariants -env doesn't remove all non-variant sites
I am using GATKv3.7, trying to remove a few samples from a big VCF file and remove all invariant sites. Here is the code I ran: java -jar GenomeAnalysisTK-3.7-0/GenomeAnalysisTK.jar -T SelectVariants...
View ArticleReverse select interval list
I have a file with RNA editing sites which I want to remove from my VCF. I can select all the RNA editing sites with: java GenomeAnalysisTK.jar \ -T SelectVariants \ -R human_g1k_v37.fasta \ -V...
View ArticleWhy does SelectVariants discard variants when the input vcf is unsorted?
I am using SelectVariants to subset based on samples, while trying to keep all variants. However, SelectVariants seems to discard variants when the input file is not sorted and an index file is...
View ArticleExtracting consensus variants from a VCF with 27 RNA-seq samples from the...
Is there a tool, or recommended best practice for generating a consensus set of variants from multiple samples of the same genotype? In short I have 27 RNA libraries from different individuals and...
View ArticleUnknown index type error of SelectVariants
Good day to you! I ran a selectvariant command by nohup java -Xmx5g -jar /home/wuwei/software/GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar -R $referrence -T SelectVariants --variant:VCF...
View ArticleSelectVariants error
I`m calling SNP by haplotype caller,and i got vcf document for each sample. After that , i use selectvariant to select variants of SNP . But i got this error: ##### ERROR...
View ArticleConvert CombineVariant output to individual vcf files
HI, I was curious if it possible to convert the output of CombineVariants back into individual sample vcf files. Based on answered questions in other threads, I am under the impression that you should...
View Articlewhat reads from original BAM are listed in mutect2 VCF-output?
Dear GATK team, I am sorry if my question is naive. After running mutect2 (version 4.2) what positions (AND corresponding reads) from the original bam-file are reported in the vcf file? all that passed...
View ArticleAbout SelectVariants
I want to filter out the variants if VAF in tumor samples was more than 0.3. Command line: gatk SelectVariants -V somatic_twofiltered.vcf -R ucsc.hg19.fasta -select...
View ArticleTroubleshooting: ERROR - variant files have inconsistent references for the...
Greetings, I am hoping to get some help troubleshooting a frustrating error I am having trying to genotype a large set of data. The source data is nearly 12000 WES samples, which were sequenced by a...
View Articlehard filtering one WGS raw.g.vcf
Hi, Im trying to apply hard filter to one WGS.g.vcf (coming form HaplotypeCaller). The command im using is: java -jar ${GATK}/GenomeAnalysisTK.jar -R ${reference}/mm10.fa -T SelectVariants -V...
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Standard practice for VCF filtering for the purpose of fingerprinting via...
Hi all, I was wondering whether I could get some insight into what the standard procedure for `fingerprinting' by prop. IBS for sequencing data is. To be more precise: the proportion IBS between the...
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Get a summary of SNV calls from MuTect2
Hello, Following the best practice of calling variants using MuTect2 with GATK3, I have stumbled upon the step 5 where we can filter our file for INDELs or SNPs. But I had issues with the contigs not...
View ArticleSelectVariants tool crashed because of error for input string.
Hi, I am trying to use GATK's SelectVariants tool to select variants of a specific sample from a vcf file that has variants for 476 different samples (it's a very large file, 14Gb). I have done this...
View ArticleFiltering VCF file to remove ./.
Hello, I am trying to understand my sample format in my merged vcf file of RNA-seq SNPs produced from the GATK best practices. I have several vcf files that I have merged into one file using...
View Articleselect private SNPs for individual samples from a multisample VCF
I'm trying to select private SNPs for each sample from a multisample VCF. Here is my workaround command: java -Xmx16G -jar GenomeAnalysisTK.jar \ -T SelectVariants \ -R ${FASTA} \ -V ${VCF} \ -o...
View ArticleThe numbers of variants in GATK SV --concordance output
what is the true meaning of SV --concordance? I have a vcf produced by GATK UG containing 5162953 variants and a vcf generated by samtools which has 244095 variants. After SV –concordance for these two...
View ArticleFiltering does not work due to missing MQ values
Hello, I'm trying to filter my VCF on MQ value. I've done it for other annotations using VariantFiltration with no problems, but MQ is just not collaborating. So first I had it in an expression with...
View ArticleCan FastaAlternateReferenceMaker put Ns instead of the reference bases where...
Dear GATK team, I'm using FastaAlternateReferenceMaker to generate a fasta file per sample. To do so, I had to first generate a vcf file per sample and use FastaAlternateReferenceMaker to generate a...
View ArticleSelectVariants exclude non-variant sites after GenotypeGVCF
Hello, GATK I merged 40 individual gvcf files with CombineGVCFs and set the Genotype with GenotypeGVCF. After that, I want to filter out those sites which have no SNPs or INDEL in all the samples. Is...
View ArticleFiltering based on annotations under ANN within the INFO field
Hello! I am brand new to using GATK and was assigned the task of filtering a VCF file provided to me. I already had success with filtering based on the AF value and other numerical fields, however, the...
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 ArticleGATK 3.5 or 3.8 dropped multiallelic variants containing both SNP and Indel
We noticed that GATK3.5 or 3.8 dropped multiallelic variants containing both SNP and Indel when selecting SNP and INDEL variants separately for filtering. We followed the DNA-seq best-practices. Our...
View ArticleGenomicsDBImport--do multiple samples need individual databases?
I am trying to do variant calling on a reference transcriptome that I've produced, but I have some questions about functionality of GenomicsDBImport, and downstream in SelectVariants. I know that you...
View ArticleMissing sample_file -sf option in GATK4 SelectVariants
In the port over to gatk SelectVariants the sample name -sn and sample expression -se options made it in, but the sample_file -sf option did not seem to make it. I tried: gatk SelectVariants \ -V...
View ArticleFilter raw.vcf (post GenotypeGVCF) with the PASS variants (post VQSR)
GATK 4.0.10.0; 105 WES Hi, after VQSR steps I went to exctract the PASS variants from the raw VCF (post GenotypeGVCF) #Raw vcf after GenotypeGVCF: raw.vcf grep -v "^#" raw.vcf | wc -l #994879 variants...
View ArticleSelectVariant (GATK 4.10.0) output site not in Interval list (?)
Hi, I have run SelectVariants just to output sites belonged to my interval list (i.e. a list of single site), which in the format like this: ... chr21:28407515 chr21:29497692 chr21:30101335...
View ArticleSelectVariants processing 0 variants with -ids rsidlist.txt \-V...
Hello, The title probably says it all, the above vcf is the second genome I have used to extract the desired rsids from using a text file with each rsid separated by a newline. In each case the...
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 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 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 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 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 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 - 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 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 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 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 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 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 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 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 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 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 ArticleWhat 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...
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