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wangc29 / MSIpred

Microsatellite instability prediction
MIT License
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MAF file #2

Open YuvaraniThambidurai opened 5 years ago

YuvaraniThambidurai commented 5 years ago

Hi I have tried to run the program MSIpred after generating MAF file for tumor only data. I used annovartomaf for generating MAF file and the resultant file column was not found to be similar with the toy.maf. I received error when I tried to create tagged toy_maf. Could u please suggest me on how to rectify the error? Thanks in advance. target_interval_tree = IntervalTree.from_tuples(interval_tuples) File "build/bdist.linux-x86_64/egg/intervaltree/intervaltree.py", line 249, in from_tuples TypeError: new() takes at most 4 arguments (6 given)

Teejay1995 commented 3 years ago

Hey Yuvarani, I recently encountered the same issue. On first check, the MAF file was clean no major discrepancies were there.

I solved the issue by simply removing the "chrMT" variants from the MAF and re-ran. It worked perfectly fine.

Reason -> simpleRepeats.txt is used for the tagging of the maf file, this error is caused because this file doesnt have any instances of mitochondrial variants.

Hope this solves the issue! Cheers!