MHC Variant Calling from Illumina PGF Data

PGF sequencing data was generated from 125 bp paired-end reads generated on the Illumina GAIIx sequencing platform. The paired-end reads were quality trimmed (minimum PHRED score of 30) using sickle version 1.010 (https://github.com/najoshi/sickle). Quality trimmed reads were aligned to the reference genome (HG19) using BWA version 0.6.2-r126 with default parameters [44 (link)]. After alignment, variant calling was performed following GATK v3 best practices with recommended parameters for accurate and efficient variant calls [45 (link)] (GATK version 1.6-2-gc2b74ec and Picard version 1.57). The only step not applied was the removal of duplicates since the target (4 Mb of the MHC) was relatively small compared to the whole human genome.