The 'TARGT' pipeline for Targeted Analysis of sequencing Reads for GenoTyping can be used for genotyping of MHC/HLA genes (or other genomic regions) from ancient and modern shotgun sequence data with moderate to low sequence coverage. The pipeline consists of a main bash script that calls the different steps of the pipeline and can either be called directly or submitted to a cluster queue system, as well as additional sub-scripts and files, that are required to perform the different steps. The pipeline also requires installed versions of the mapping tool Bowtie2 and samtools.

Features

  • Genotyping of HLA genes from low-coverage sequence data
  • HLA allele calling from ancient DNA
  • Works for both ancient and modern DNA data
  • Can be adapted to other target regions easily

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Registered

2019-08-06