At MD Anderson , raw sequencing data were converted to a fastq format and aligned to the human genome ( hg19 , GRCh37 ) using the BWA - MEM algorithm . The aligned BAM files were processed using Picard and GATK with default parameters and then variants were called using MuTect and Pindel against pooled unmatched normal sequences developed in - house . Variants with low - quality sequencing , no obvious protein - coding change or common polymorphisms with a population frequency of 0.14 % in public variant databases were filtered out .