ADTEx - Tutorial

Home > Tutorial

ADTEx accepts either BAM files or coverage files generated by BEDTools of the tumour and control (matched normal) samples.

coverageBed –abam <BAM input> -b <targets in bed format> -d > <output.file>

Variations of input files for the above command can be found in BEDTool’s documentation. However, the option (-d) should be used.
The output of this command should look like the following without headers:

This will have the targets of the exome capture in BED format (http://genome.ucsc.edu/FAQ/FAQformat)
All chromosome definitions should be in the same format as the BAM or DOC file (i.e. ‘1’ or ‘chr1’ for chromosome 1).

B allele frequencies fileThis is a tab delimited file with following essential headers.

Tab delimited ‘cnv.result’ file - The result will have copy number prediction for each exon. This will have other information such as chromosome, exon start, exon end, DOC ratio after mean normalization, and segment mean in tab delimited format.
Plots of CNVs and genotypes results - If plotting option is specified in the command, this will plot DOC ratios for each chromosome separately as ‘.png’ file. The segments will be coloured based on the predicted copy number. Plots will also be generated for genotypes separately for each chromosome as ‘.png’ files and combined ‘.pdf’ file of all images.
Tab delimited ‘zygosity.res’ file - This has zygosity state of each heterozygous SNP locus.
Normal cell contamination prediction in a separate file

--normal / -n <input file>	Input file for matched normal [required]
--tumor / -t <input file>	Input file for tumor [required]
--bed / -b <input file>	Target definitions [required]
--out / -o <output folder>	Output folder path [required] (Programme will create a folder with this name, so it must not be a name of a existing folder)
--DOC	Specify whether tumor and matched normal input give coverage information [required only when input in DOC format]
--ploidy	Common ploidy of the tumor [optional]. Default: 2
--estimatePloidy	This will estimate base ploidy when --ploidy option is not provided. However, --baf must be provided to execute this command [optional]. Default : False
--plot / -p	If specified, the output plots will be generated. [optional]
--minReadDepth	Exons having avg. reads <minReadDepth in the control sample will not be analysed [optional]. Default: 10
--baf	If specified BAFs will be used to predict zygosity states and correction of copy number predictions [option al]. The B allele frequency file should be specified with this option.

python ADTEx.py --normal normal_sample.BAM --tumor tumor_sample.BAM --bed target.bed --out output_folder

python ADTEx.py --normal normal_sample --tumor tumor_sample --bed target.bed --out output_folder --DOC

python ADTEx.py --normal normal_sample.BAM --tumor tumor_sample.BAM --bed target.bed --out output_folder --baf file.baf

python ADTEx.py --normal normal_sample.BAM --tumor tumor_sample.BAM --bed target.bed --out output_folder --baf file.baf --estimatePloidy