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["Variable","Method of Calculation"]
["Reference Allele Count","Generated using mpileup from Samtools (v.0.1.18)"]
["Non-reference Allele Count","Generated using mpileup from Samtools (v.0.1.18)"]
["Sum of Base Qualities","Generated using mpileup from Samtools (v.0.1.18)"]
["Tumour Coverage","Generated using BEDTools coverage (v2.18.2)"]
["Normal Coverage","Generated using BEDTools coverage (v2.18.2)"]
["Mapping Quality","Generated by converting BAM file to BED file using BEDTools bamtobed (v2.18.2) and median quality score calculated using BEDTools groupby (v2.18.2)"]
["Median Read Position","Generated using Bio-SamTools Pileup (v1.39)"]
["Homopolymer Rate","Measured over 201 bp window (+/- 100 bp from position) determined using BEDTools getfasta (v2.18.2). Measured using following equation where n represents the number of bases in each homopolymer and N represents the number of homopolymers:  (ΣNi=1 ni2) / N"]
["GC Content","Measured over 201 bp window (+/- 100 bp from position) determined using BEDTools getfasta (v2.18.2). Measured using following equation: #GC/window length"]
["Trinucleotide Sequence","Generated using BEDTools getfasta (v2.18.2)"]
["Genomic Element","Generated using Annovar (v.2012-10-23) geneanno using database type 'refgene' and build version 'hg19'"]
["Distance to Nearest Germline SNP","Germline SNPs determined using GATK UnifiedGenotyper, VariantRecalibrator and ApplyRecalibration (v2.4.9). Distance to closest SNP generated using BEDTools closest (v2.18.2)"]
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