title: WXS of Capan-1 cell line
design: GATK best practices for WXS were followed. Briefly: an unmapped BAM file was created from forward and reverse Fastq files. Illumina adapters were marked. The unmapped BAM file was mapped to hg38.v1.vd1 with BWA and sorted with SortSam. the sorted BAM and unmapped BAM were merged with GATK MergeBamAllignment, during which overlapping reads were clipped. the merged BAM file was sorted (SortSam), duplicates were marked (GATK MarkDuplicates), Nm, Md and Uq Tags were added and readgroups were set before base quality score was recalibrated with GATK BaseRecalibrator.