Fig. 2

Flow chart of the generic variant calling pipeline featured in AMLVaran. An uploaded bam-file is processed by an arbitrary number of variant calling tools (configurable by templates). The resulting variant lists are then normalized and integrated into one common list (in vcf format). For the resulting list of variants, a functional annotation via SNPeff [12] and a calculation of sample-specific quality parameters (such as allelic frequency, base quality, etc.) from the bam file is performed via bam-readcount [27]. By means of a basic filter, low quality variants are excluded. For the remaining ones, an effect prediction using Provean [28] is carried out. The resulting data is stored in a database and then processed by an advanced filtering strategy