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**Additional file 1.** NGS raw data processing methods: The additional file provides step-by-step instructions of the bioinformatics pipeline to be used for the raw data processing, including feature-based statistical testing and normalization of the raw data and optionally after the pipeline pre-processing. (PDF 474 kb)
BWA
: Burrows–Wheeler Aligner
bp
: Base pair
CAS
: Casetta
DFT
: Derivative Fast Transform
GUI
: Graphical User Interface
IGV
: Integrative Genomics Viewer
IRX
: Irregularity
IQR
: Interquartile Range
MAF
: Minor allele frequency
MDA
: Multiple Displacement Amplification
NGS
: Next Generation Sequencing
PED
: Pedigree
QC
: Quality Check
RMF
: RMS
RSS
: Relative Strand Specificity
SRA
: Short Read Archive
ST
: Standard
STAS
: Statistical Testing of Allele Specificity
STAS
: Statistical Testing of Allele Specificity
TDF
: Tail/Dot File
TREO
: Total Reference Equivalent Output
**Electronic supplementary material**
The online version of this article (10.1186/s12864-017-4146-x) contains supplementary material, which is available to authorized users.
We thank the four reviewers for the careful and constructive feedback, which has helped us to improve the manuscript. We are grateful to all members of the Sanger Institute MPSN, especially to Phil Carlson for the development of the software pipeline and Giorgio Pergolini for his continuous support.
Availability and
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