Raw variant calls from the Sheep genomes project - Run1

Raw variant discovery using multiple sheep breeds - Run1: Fastq files were aligned to Ovis aries reference genome version 3.1 using bwa mem. Duplicates were removed using Samtools rmdup. Local realignment around indels was performed using GATK tools RealignerTargetCreator and IndelRealigner. Variant calling on resulting BAM files was conducted independently using both Samtools mpileup and GATK Unified Genotyper. A union set of the Samtools and GATK called variants was produced using GATK CombineVariants to produce the final VCF files. (Software: bwa-0.7.12,GATK-3.4-46,samtools-1.2+htslib-1.2.1)