WGS of human melanocytes
DNA of three cell lines were isolated using Purelink Genomic DNA Kit (ThermoFisher). The NanoDrop was used to quantify DNA amount and quality. DNA samples were sequenced at 50X depth with an Illumina HiSeq sequencer generating 150 bp paired reads (PE150). Raw FASTQ readings were quality controlled using the fastQC program. They were also pre-processed using the "Trim Galore!". FASTQ files were aligned to the GRCh38 reference genome using the optimized BWA-MEM algorithm and post-processed according to the GATK 3.7 best-practices protocol (duplicate marking, recalibration, realignment). SNP and INDEL variants were detected using a variant caller reimplementing the algorithms of GATK HaplotypeCaller and GATK GVCFtyper. This application returns the resulting files in BAM, gVCF and VCF format. Then, to improve the precision of SNP and INDEL variant detection.