Novogene_WGS

The following repisitory contains scripts used for processing of Novogene WGS data produced for Zosterops lateralis (and other avian species). Currently scripts will take raw sequencing reads all the way to producing VCF files for downstream analyses.

1. InitialQC.sh - conduct intial quality check using FastQC
2. Filter_Reads.sh - filter raw sequencing reads to remove low quality base calls and remove adapter content
3. SecondaryQC.sh - conduct secondary quality check of filtered sequencing reads
4. Map_sample_reads.sh - map filtered reads to reference genome (outputs multiple bam files per individual)
5. Create_Single_Sample_Bam.sh - merge multiple bam files to generate a single bam for each individual
6. Sample_Genotyping.sh - conduct inidivual sample genotyping using GATK haplotype caller
7. Merge_gVCFs.sh - merge individual sample gVCFs into a multi-sample intermediate gVCF file
8. Joint_Genotyping.sh - perform joint genotyping using GATK GenotypeGVCFs tool