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pyc1216 / hlaloh-pipeline

hla-typing by optitype & polysolver , detect loh by lohhla.
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issue in get_result.py #1

Open MagicalLily opened 1 year ago

MagicalLily commented 1 year ago

Hello, if the HLA allele of LossAllele column matches the HLA allele of HLA_A_type1 column, should the LOH be determined based on PVal_unique<0.01 and HLA_type1copyNum_withBAFBin < -1？

Best wishes! Lily

pyc1216 commented 1 year ago

Hello, Thank you for Pointing out the problem. If LossAllele = HLA_A_type1, check HLA_type1copyNum_withBAFBin < -1, else check HLA_type2copyNum_withBAFBin. My script does not consider this situation. I will correct it later.

Best wishes!

xiasijian commented 1 year ago

image I have no idea that you use log2.

pyc1216 commented 5 months ago

image I have no idea that you use log2.

"You are right, log2 should not be used here. In some samples, HLA_type1copyNum_withBAFBin and HLA_type2copyNum_withBAFBin are calculated as negative numbers. I don't understand the reason for this, which was why I used log2 at that time."