Any aligner that produce
BAM files can be used to align the reads to the reference genome. The
method is tested with BAM files generated by BWA.
Can I use a pooled normal instead of a matched normal?
ADTEx is mainly developed
for paired tumour and matched normal samples. However, a pooled normal
sample can be used as long as they have been generated using the same
capture platform as the tumour sample.
ADTEx only works on human whole exome data?
ADTEx has been tested on
human and mouse data both whole exome and custom capture. However,
ADTEx works better with whole exome sequencing data.
4. How can I cite ADTEx in my paper?
Amarasinghe KC, Li J,
Hunter SM, Ryland GL, Cowin PA, Campbell IG and Halgamuge SK: Inferring
copy number and genotype in tumour exome data. BMC Genomics 2014,
15:732 doi: 10.1186/1471-2164-15-732
Previous related work:
Amarasinghe KC, Li J and
Halgamuge SK: CoNVEX: copy number variation estimation in exome
sequencing data using HMM. BMC Bioinformatics
2013, 14(Suppl 2):S2 doi: 10.1186/1471-2105-14-S2-S2