ALT field in vcf is a *
My variant call set contains SNP calls which have a "*" listed as alternative allele (field 5 in the vcf) which isn't specified in the vcf specifications. I have noticed that they generally appear in...
View ArticleWhy Mutect2 calling only germline SNV from normal-tumor datsets ?
Hi I called variants using mutect2 from normal and tumor samples. I'm surprised it showed all germ-line variants cant find single somatic variant . Whether I missed any parameters ? how to sort out...
View ArticleEnsembl GRCh38 indels and dsnp vcf files
Hello, I am using GATK3.8 to call variants in RNA-seq data. I am following the best practices for RNA-seq (https://software.broadinstitute.org/gatk/documentation/article.php?id=3891). My problem is...
View ArticleLiftOverVcf Not Working
Hello: Getting an error with LiftoverVcf. The Output Seems to have most of the information about my Java and such. Including all the other relevant information i could find - chain file i am using,...
View ArticleDoes ReadBackedPhasing rely on a VCF's GT field?
I have a VCF file that is missing the GT field. Can I just add 0/1 for each variant, and let GATK's ReadBackedPhasing take care of resolving the actual phased genotypes?
View ArticleIs it possible to recalculate QUAL on a subset of samples?
I have a joint-called VCF of 100s of samples in different pedigrees. For my analysis, I have to split the joint VCF into pedigrees. However, I would like to recalculate the QUAL scores for the pedigree...
View ArticleVCF contigs don't match reference genome
Hello, I am working with fungi RNA-seq SNPs that I called using the GATK best practices pipeline. I have 12 vcf files of SNPs that I called using REFERENCE1.fa. I also have a vcf file from a...
View ArticlegetPileupSummaries input for hg38
Hi- I would like to run getPileupSummaries on bam files aligned against hg38. Do you have any recommendation about what vcf input to use for hg38? The docs relative to getPileupSummaries suggest using...
View ArticlePopulation frequency in MuTect2
I am running MuTect2 with GATK4 in tumor only mode but the SNPs in my vcfs are not labelled with their rs number or population frequency. Here is the command I am using. gatk Mutect2 \ -L...
View ArticleTabix-incompatible file creation times
I have a workflow that indexes a vcf.gz to produce a tabix index (tbi). A common sanity check when reading from a VCF index is to verify that the index was created more recently than the VCF. It seems...
View ArticleDifference in GenotypeGVCFs generated VCF after consolidation with...
Hi, I had a set of total 81 GVCFs that I first consolidated using GenomicsDBimport and then using CombineGVCF and then GenotypeGVCF was run in both cases. For GenomicsDBimport, I ran the command per...
View Article2/50 ind show ./. at almost all positions in final vcf even though there is data
I used HaplotypeCaller to generate VCF from 50 individuals. My reference is Rattus norvegicus and 48/50 individuals are Rattus norvegicus. The remaining two individuals are Rattus rattus species. The...
View ArticleMerge VCF Files
Hello, BACKGROUND: I am working with a public data set that consists of VCF files. ( I cannot go back upstream in the process). VCF files are broken out by patient sample. And broken out further by...
View ArticleHaplotypeCaller output header and one position recode without error
I'm trying to run gatk4 HaplotypeCaller using the following command: ./gatk HaplotypeCaller -R ./reference.fasta --emit-ref-confidence GVCF --dbsnp ./samtools_gatk_common.vcf -I ./sample.bqsr.bam -O...
View ArticleASEReadCounter ouputs only header without error
Hi, I have a problem similar to this: HaplotypeCaller output header and one position recode without error but with GATK4 ASEReadCounter. I have VCF file created using Samtools mpileup, compressed with...
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Using VariantEval
This article has been deprecated in favor of a new method article which you can view here. For a complete, detailed argument reference, refer to the technical documentation page. Modules You can find...
View ArticleCollected FAQs about VCF files
1. What file formats do you support for variant callsets? We support the Variant Call Format (VCF) for variant callsets. No other file formats are supported. 2. How can I know if my VCF file is valid?...
View ArticleABHom Annotation Formula
Hello, For the “ABHom” annotations, the VCF header gives the following formula : (A/(A+O)). What does the 'O' stand for? Thanks, Mika
View ArticleContributing to the GATK: VCF as XML
Hi the GATK team, I hate the VCF format :-) I want a structured output and I'd like to promote the use of the XML/JSON to store the variations. I think the best way to achieve this, is to integrate...
View ArticleMerge BAM to VCF. Which is the best workflow?
Dear All, I am very new to the analysis of NGS data. I would like to merge the information of sample 1029 from HGDP (http://cdna.eva.mpg.de/denisova/VCF/human/HGDP01029.hg19_1000g.12.mod.vcf.gz) to SAN...
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