Variant discovery from whole genome sequence data from a commercial broiler line and a CSFIR- mApple reporter transgenic layer line

Abstract

The data comprises variants calls from whole genome sequencing (WGS) data from a set of founder broilers (n=10) and transgenic layers (n=10). The broiler samples belong to commercial Ross 308 founder population and were sourced from PD Hook (Hatcheries) Ltd, Cote, Brampton, Oxfordshire, UK. The layer samples belong to founder population from a CSF1R-mApple reporter transgenic layer line on an ISA-Brown genetic background and were produced in The Roslin Institute. WGS was performed on Illumina HiSeqX platform in paired-end mode with read length of 150bp. After quality checking (using FASTQC v0.11.8) and trimming of poor quality data (using Trimmomatic software v3.5 and with trimming criteria: LEADING:20, SLIDINGWINDOW:10:20, MINLEN:50), sequence reads were mapped against chicken reference genome (Galgal5.0) using BWA_MEM algorithm (v0.7.8). Before proceeding to variant calling, the mapped reads in BAM files were further processed for marking duplicates (using Picard tools v2.1.1) and indel realignment (using GATK v 3.7.0). Variant calling was performed using samtools mpileup (v 1.1) in conjunction with bcftools with minimum base and mapping qualities set to 20. The variant data is present in the Variant Calling Format (VCF). ## Broiler samples: ## sample1662 (Male (M)), sample1674 (Female (F)), sample1678 (F), sample1679 (F), sample1684 (F), sample1686 (F), sample1687 (M), sample1696 (M), sample1697 (M), sample1698 (M). ## Transgenic layer samples: ## sample14 (F), sample16 (F), sample18 (M), sample24 (F), sample26 (M), sample29 (F), sample4937 (M), sample4946 (M), sample4 (F), sample6 (M).