Example delta smelt GT-seq dataset for gtseq_microhap

Example paired-end GT-seq dataset for demonstrating the gtseq_microhap Direct microhaplotype genotyping pipeline. The dataset contains paired-end FASTQ files from 96 delta smelt (Hypomesus transpacificus) individuals genotyped with a 410-locus GT-seq panel. Reads were subsampled to 150,000 read pairs per sample to reduce download size whilepreserving locus representation and genotype structure. The dataset now includes scripts for PIC of highestMAF_snps vs microhaps, concordance testing of bwa derived genotypes versus direct microhaplotype genotyping, and read depth versus genotype concordance / call rate. The dataset includes: - dsm_gteseq_microhap_dataset.tgz Subsampled paired-end FASTQ files. - dsm_GTseq410_Primers-notag.csv Primer definition file required by the pipeline. - gtseq_microhap_readme.txt Instructions for running the example dataset. -gtseq_microhap_v0.3.1_validation.tgz scripts and instructions for reproducing method validation results The gtseq_microhap software is available at: https://github.com/GTseq/gtseq_microhap