I am confused whether some of the mutations reported in some big study like CCLE are artifactual mutations. I have been asked this question many a times, but don't understand what artifactual mutations are ?
Are artifactual mutations related to:
platform related - eg. illumina, 454 etc
protocol related - eg. library preparation for rna-seq or exome-seq purposes
variant calling algorithm related - eg GATK , SAMTOOLS mpileup
or something else what I mite be missing
Please shed some light on this topic.