Open firatuyulur opened 3 years ago
The warnings are indicating mutations that are excluded because harborer in genomic regions for which state trees are not available in the default "state tree" file. In order to fix this, you should generate new state trees according to the copy number states that you have in your input. Please follow the new instructions and scripts from @brian-arnold to achieve this at:
https://github.com/raphael-group/decifer#optionaldata
Please let us know if you have any further issue.
In the 'scripts' subdirectory, we've added a new script to generate the input file for decifer using SNV data (in standard VCF format) and CNA data (from e.g. HATCHet). As we describe, this script also generates a file called cn_states.txt that may be given directly to the generatestatetrees function on the command line to generate the state trees observed in your specific data.
Please note that this function may take a very long time to complete if the total copy number is high for a particular clone (e.g. total copy number > 6). However, even if you are able to get the state trees for them, estimates of the CCF/DCF for SNVs in a region with very high total copy number may be much less inaccurate, since there's more uncertainty in what the VAF -> CCF/DCF transformation is (as described in the manuscript) for these sites.
Hi, I'm tyring to run decifer on some TRACERx 100 data but I either lose some mutations or get the
list index out of range
error.The sample that I am losing mutations but still get a result is CRUK0036. Here is what the first few lines look like in the stdout
I have around 250 input SNVs for CRUK0036, yet decifer results have about 140 snvs. Do you know why this happens?
For CRUK0039, I once again receive many warning lines just like CRUK0036 and it fails to produce a result with the following error.
I've attached the input files for each sample as well as the missing SNVs for CRUK0036 in case it is helpful.
Thanks Firat
CRUK0036_missing_snvs.txt CRUK0036.zip CRUK0039.zip