Standard Operating Procedure, Scripts, and data for GT-seq Genotyping
Repository Contents:
(1) Example Protocol: Full genotyping pipeline from raw sequence reads to fully filtered SNP dataset in multiple formats. Download and open GT-seq_SOP.html in a browser to view. To run for yourself the easiest path is to clone this full repository to your local machine.
(2) Example Data: data to run the example protocol/SOP
(3) Probe Sequences Data needed to run pipeline
(4) GT-seq Scripts: Updated repository of GTseq pipeline scripts
(5) Panel Info: Information about markers such as primer sequences, source, annotation etc
(6) Panel Mapping: Results from mapping GTseq marker amplicons against reference genomes
(7) Primer Pools: Different pools of primers are sometimes used across runs and are indicated in illumina run summary documents. These list the markers used in the pools.