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secastel / phaser

phasing and Allele Specific Expression from RNA-seq
GNU General Public License v3.0
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parameter '--no_gw_phase 0' #79

Closed shiwobu closed 1 year ago

shiwobu commented 1 year ago

Dear Dr. Stephane: Hello, I am a graduate student of Huazhong Agricultural University. I would like to ask you a question. Recently, when I was using the software phASER, I manually phased the VCF file. I don't want the software to phase again. I am following the step-by-step tutorial you wrote, I found the relevant parameter '--no_gw_phase 0' in tutorial, but I didn't find this parameter when running the software, and there is no such parameter in the python code. What should I do? Thank you for sparing a time to read my message in the midst of pressing affairs. Best wishes

secastel commented 1 year ago

Hello - phASER will change phase only of variants where the sequencing reads support an alternative phase. Unfortunately it is not possible to disable this functionality, as this step is required building the haplotype counts. The parameter you are referring to will not prevent phasing from occurring.

shiwobu commented 1 year ago

Thank you very much for your reply and help!