PureCN implementation of ABSOLUTE as input for phylogicNDT

[naumenko-sa]

Hello!

Thanks for developing and supporting PhylogicNDT.

I used PureCN (based on ABSOLUTE ideas to generate input for PhylogicNDT):
https://bioconductor.org/packages/release/bioc/html/PureCN.html

Namely, I used this https://github.com/naumenko-sa/bioscripts/blob/master/phylogicndt/purecn2phylogicndt.R
script to select columns for files with variants and segments. Also, I was using purity information from PureCN.

My samples.sif file:

sample_id	maf_fn	seg_fn	purity	timepoint
s1	s1.maf.tsv	s1.cn.tsv	0.89	1
s2	s2.maf.tsv	s2.cn.tsv	0.68	1
s3	s3.maf.tsv	s3.cn.tsv	0.94	1

maf_fn file format:

Hugo_Symbol	Chromosome	Start_position	Reference_Allele	Tumor_Seq_Allele2	t_ref_count	t_alt_count	local_cn_a1	local_cn_a2

seg_fn file format as in the example:
https://github.com/broadinstitute/PhylogicNDT/blob/master/ExampleData/Simulations/Example_SegFile.txt

ID	Chromosome	Start_position	End_Position	A1_CN	A2_CN

PhylogicNDT call (clustering and tree building):

PhylogicNDT.py \
Cluster \
-i project \
-sif samples.sif \
--maf_input_type calc_ccf \
-rb

I'm getting a parsing error:

  File "/PhylogicNDT/data/Sample.py", line 478, in _resolve_CnEvents
    start = int(row['Start.bp'])

https://github.com/broadinstitute/PhylogicNDT/blob/master/data/Sample.py#L478

PhylogicNDT interprets it as alleliccapseg format which is different from what I've generated.
How to force timing format for CN files?

When running without CN files phylogic_report.html has been generated (but CNVs were not mapped).

Does anybody else have experience using PureCN output as input for PhylogicNDT?

Thanks!
Sergey

[Salaheddinekacimi]

@naumenko-sa running through the same issue. Have you found a way to fix this?