final VCF output with all variant and non-variant sites which passed quality control of the filtering step. The pipeline was designed in compliance with GATK Best Practices recommendations for NGS data processing. Single nucleotide variants (SNVs) and indels were called using GATK HaplotypeCaller with subsequent VQSR using a threshold of 99.9, HapMap 3.3, 1000G Omni 2.5, 1000G Phase 1 High Confidence and dbSNP build 151 training sets for SNV mode and Mills and 1000G Gold Standard Indels with dbSNP build 151 training sets for INDEL mode.
