unconverted.log
mdeloger opened this issue · comments
Hi @KyleGao ,
Is there a way to understand why a segment was not converted and if in some way a fine-tuning of a parameter may overcome this unconversion, please ?
For example an hg19 to hg38 conversion gave me :
chromosome start end same_chr/new_chr length_ratio/new_pos file
chr1 144854271 152052338 True 0.4237 input_dir/GE2486-Tumor_subclonal_allele_spe_cnv_0.43cellularity_2ploidy.transformed.txt
chr1 144621642 153916821 True 3.6042 input_dir/GE3344-Tumor_subclonal_allele_spe_cnv_0.55cellularity_2ploidy.transformed.txt
Thank you in advance for your help
Use the option --beta 4, this should solve your problem.
These segments were excluded because of their dramatic change in length, shown as the length_ratio 0.4237 and 3.6042.
This filtering is controlled by parameter beta:
--beta FLOAT Parameter in quality control.
The default value is 2 and the condition is:
1/beta < length(original segment)/length(new segment) < beta
Oh ok, I will try :-)
Thank you very much for your explanation.
Best regards