config.ini

[mattloose]

Please can you provide documentation on how to specify a config.ini file or equivalent for reference genomes other than the recommended download. The software appears hardcoded to expect chromosomes labelled as "1,2,3,4" etc.

[lavenderyuuu]

Hi Thank you for the post. The following is the documentation of how to generate a reference genome to be used in part of the workflow. prerequisite: samtools, python3

1. generate alignment (.bam) file using your own reference fasta (Grch37, hg19, hg38 or whatever you preffer) and minimap2 (please keep in mind to use this same reference fasta for the entire SENSV command)
2. put all the bam file absolute path to one single file (i.e., named it bams.txt) one line by one another
3. Generate depth file for each bam file, and then generate the reference by running the following command (in the depth_reference folder)
   1. python gen_depth_all.py [window_size] [output_directory] [bams.txt]
   2. the smaller the window size, the longer it takes
   3. the more the bam files, the longer it takes
4. After the reference is created, change the reference in the following line in "sensv" file with the reference.csv absolute path
   1. set_var("depth", "depth_ref", f'GRCh{ref_ver}.depth_ref.csv')

[fabrimafe]

Where is the file gen_depth_all.py? I can't find it anywhere. I can't find a depth_reference folder either (there is only a depth folder).

And more in general: the tool can only be used for the references you used for mapping the 24 individuals, right? It cannot be used for any genome. So, why even giving the "reference file" option?

@mattloose : were you able to solve this?