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origin: broadgsa/gatk-protected. @Test public void testHeadersWhereOneIsAStrictSubsetOfTheOther() { VCFHeader one = createHeader(VCF4headerStrings)...

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This is the documentation for the Nextflow 2018 Hackaton for beginners. This project will cover the implementation of a Variant Calling analisys pipeline for RNAseq data based on GATK best practices and using Nextflow as the pipeline framework.

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Merge Vcard files into Single VCF file with advanced Merge Vcard Pro tool. Merge Vcard Tool to Merge Multiple VCF Files. Your search for a reliable vCard merge program is over now.

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Understanding the VCF format and the haplotype representation. INFO keys used for structural variants. FORMAT keys used for structural variants. Representing variation in VCF records.· As of GATK 2.1, when merging multiple VCF records at a site, the combined VCF record has the QUAL of the first VCF record with a non-MISSING QUAL value. The previous behavior was to take the max QUAL, which resulted in sometime strange downstream confusion. Input. One or more variant sets to combine. Output. A combined VCF. Examples

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Steps to create VCF format. Initial round of lobSTR allelotyping to generate priors on allele frequencies Second round of lobSTR calling to generate genotype likelihoods and posteriors for all possible...

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• Recalibration using GATK. CountCovariates is multithreaded at the time of writing this document, but TableRecalibration is not. So, only part of the process is affected by an increase in threads. Users can speed up recalibration to some extent by increasing GATK_THREADS. • VCF Calls by GATK.

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