Merging batched call sets
Merging batched call sets Contents 1 Introduction 2 Creating the master set of sites: SNPs and Indels 3 Genotyping your samples at these sites 4 (Optional) Merging the sample VCFs together 5 General...
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Using VariantEval
For a complete, detailed argument reference, refer to the technical documentation page. Modules Stratification modules AlleleFrequency AlleleCount CompRod Contig CpG Degeneracy EvalRod Filter...
View ArticleUsing Variant Filtration
VariantFiltration For a complete, detailed argument reference, refer to the GATK document page here. The documentation for Using JEXL expressions within the GATK contains very important information...
View ArticleUsing CombineVariants
1. About CombineVariants This tool combines VCF records from different sources. Any (unique) name can be used to bind your rod data and any number of sources can be input. This tool currently supports...
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 ArticleProblem to merge vcf files
Dear team, I am new to GATK and I am having a hard time simply trying to merge vcf files. I have tried to solve the problem by referring to the guide and to previous posts, but nothing woked. Actually...
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 ArticleFiltering VCF files
I have used the UnifiedGenotyper to call variants on a set of ~2400 genes (TruSeq Illumina data) from 28 different samples mapped against a preliminary draft genome. I do not have a defined set of SNPs...
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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Using Variant Annotator
2 SNPs with significant strand bias Several SNPs with excessive coverage For a complete, detailed argument reference, refer to the GATK document page here. Introduction In addition to true variation,...
View ArticleCan compression of VCFs (when specifying output file as .vcf.gz) be improved?
This is not a bug per se in that it does not cause incorrect output, but I think it would be accurately described as an "unintended consequence" of very poorly compressed VCF output files. GATK allows...
View ArticleBest way to get additional annotations?
Broad recommends using snpEff to add annotations to VCF files created by GATK. This gives annotations about the effect of a given variant: is it in a coding region? Does it cause a frameshift? What...
View ArticleInterface with BEAGLE Software
Interface with BEAGLE imputation software - GSA Contents 1 Introduction 2 Example Usage 2.1 Producing Beagle input likelihoods file 2.2 Running Beagle 2.2.1 About Beagle memory usage 2.3 Processing...
View ArticleForce CombineVariants to treat all vcfs as single sample
I am trying to merge two vcfs (SNVs and INDELs) from the same sample. The problem appears to be that the INDEL vcf defines "combined_sample_name" but the SNV vcf does not. So when I merge I get two...
View ArticleUsing GATK convert ped to vcf
Before there is webpage for how to convert plink ped format to vcf format. But it seems that this link disappeared. http://www.broadinstitute.org/gsa/wiki/index.php/Converting_ped_to_vcf Thank you very...
View ArticleDifferent annotations for same co-ordinates in vcf
Please look at lines 1 and 2 taken from a vcf file, which have same Chromosome and Position and one of the Alt allele is same in both lines, different allele count and have different rsID. 1 1229111...
View ArticleEmpty VCF file from GATK-Lite UnifiedGenotyper
(There was another question about a similar symptom, but the answer does not appear to apply to what I'm seeing.) I get an empty VCF file that just contains the header lines. The input VCF file is...
View ArticleDisagreement between HaplotypeCaller, VariantAnnotator, and ValidateVariants...
I ran the HaplotypeCaller, VariantAnnotator, and Variant Validatoor on chr3 locations from a human tumor sample. The HaplotypeCaller command line is:...
View ArticleUsing SelectVariants
SelectVariants SelectVariants is a GATK tool used to subset a VCF file by many arbitrary criteria listed in the command line options below. The output VCF wiil have the AN (number of alleles), AC...
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