PREFACE config file

[smruti241]

I want to know how to prepare config file from wisecondorX results or how to parse BAM files to obtain good FFY measure? Because I want to prepare config file from wisecondorX results, in case of unknown samples with unknown gender. Please guide me regarding this because I want to use this preferably for wisecondorX.

[KhanhLPBao]

Hi @smruti241
Do you mean the .bed file contains log2 records of each bins? WisecondorX cannot calculate FFY, even with the reference file made from all male samples and without --nipt, it returned with error. I'm looking for another program but not found anyone yet, so maybe we should keep this topic until someone or us find another program that can calculate FFY. Now I'm trying to use FFX prediction but its results compared with seqff is not the same in many cases

[smruti241]

wisecondorX gives only z-score, not fetal fraction for y and X. I am asking about preface config file. How to prepare it if I have samples with unknown gender?

[KhanhLPBao]

@smruti241 on output file from WisecondorX predict, there is a _bins.bed file. You create .bed file from that file by typing this command:
cut -f1,2,3,5 [filename]_bins.bed > [othername].bed

[smruti241]

What about config file? I am not asking input bed file. Please tell me about config file