Getting the ploidy of tumour

cancerit / ascatNgs

Somatic copy number analysis using WGS paired end wholegenome sequencing

http://cancerit.github.io/ascatNgs/

GNU Affero General Public License v3.0

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Getting the ploidy of tumour #88

Closed beginner984 closed 5 years ago

beginner984 commented 5 years ago

The only thing I have is the output of scatngs like below

Chromosome  Start   End Total_CN    Minor_CN
1   16298   12889922    2   1
1   12890791    13182878    3   1
1   13182899    22208689    2   1
1   22210044    22360814    3   1
1   22361313    31163036    2   1

Could I infer tumour ploidy from this data please?

keiranmraine commented 5 years ago

You should have a text file *.samplestatistics.txt:

NormalContamination 0
Ploidy 3.79736096337017
rho 1
psi 3.65
goodnessOfFit 97.9828769860925
GenderChr Y
GenderChrFound Y

For additional information see the protocols paper linked from the wiki