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getzlab / deTiN

DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.
BSD 3-Clause "New" or "Revised" License
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Running with SSNV data only #27

Open jonMitchGEL opened 4 years ago

jonMitchGEL commented 4 years ago

I was wondering if and how it's possible to run deTiN using only SSNV data.

Running deTiN without any input produces the error message

"One of CN data or SSNV data are required."

implying that it should be possible to run with SSNV data only. When I try this I get

Traceback (most recent call last): File "/home/jmitchell1/deTiN_env27/bin/deTiN", line 8, in <module> sys.exit(main()) File "/home/jmitchell1/deTiN_env27/local/lib/python2.7/site-packages/deTiN/deTiN.py", line 462, in main di.read_and_preprocess_SSNVs() File "/home/jmitchell1/deTiN_env27/local/lib/python2.7/site-packages/deTiN/deTiN.py", line 195, in read_and_preprocess_SSNVs self.annotate_call_stats_with_allelic_cn_data() File "/home/jmitchell1/deTiN_env27/local/lib/python2.7/site-packages/deTiN/deTiN.py", line 172, in annotate_call_stats_with_allelic_cn_data self.call_stats_table['tau'] = tau File "/home/jmitchell1/deTiN_env27/local/lib/python2.7/site-packages/pandas/core/frame.py", line 3370, in __setitem__ self._set_item(key, value) File "/home/jmitchell1/deTiN_env27/local/lib/python2.7/site-packages/pandas/core/frame.py", line 3444, in _set_item self._ensure_valid_index(value) File "/home/jmitchell1/deTiN_env27/local/lib/python2.7/site-packages/pandas/core/frame.py", line 3424, in _ensure_valid_index value = Series(value) File "/home/jmitchell1/deTiN_env27/local/lib/python2.7/site-packages/pandas/core/series.py", line 262, in __init__ raise_cast_failure=True) File "/home/jmitchell1/deTiN_env27/local/lib/python2.7/site-packages/pandas/core/internals/construction.py", line 658, in sanitize_array raise Exception('Data must be 1-dimensional') Exception: Data must be 1-dimensional

which looks like it's expecting the CN data.

Is it poossible to run with the --mutation_data_path file only and if so do you have any suggestions as to what I might be doing wrong?

Thanks very much.

amarotaylor commented 4 years ago

Hey Jonathan

I’m out of town this weekend I can take a look at this on Monday. If you need to move forward you could pass a dummy copy number file where the copy number is 2 and minor allele fraction is 0.5 for each segment. Without copy number data detin would make this assumption internally anyway. Hope that helps

jonMitchGEL commented 4 years ago

Thanks Amaro. That's already very useful. The quick response is appreciated.

shashwatsahay commented 1 month ago

Hi

was this ever resolved, because i am assuming that if we only run via ssnv then we dont have a hetsnv file also