example run?

[brettva]

Hi,

I seem to be having a lot of trouble getting this to run, example command with example input and output files might help with troubleshooting. Would this be possible? Thank you.

[ardalan-n]

Hi, Thank you for your interest in our program. I'll try to add some examples soon. Meanwhile, I hope the following description can be helpful: The current version assumes the VCF files are provided in 22 separate files (one file for each chromosome) and they all have a similar prefix. For example, assume you can have all the VCF files for each chromosome in a folder called ../myfiles/, and the file names are as follows:

panel1_chr1.vcf.gz
panel1_chr2.vcf.gz
...
panel1_Chr22.vcf.gz

Then the arguments would be: -i ../myfiles/ -v panel1_chr -g ../my_mapping_files/

-gshould point to a folder containing all genetic mapping files for the VCF inputs (../my_mapping_files/). For each chromosome, you need to provide a genetic mapping file that has the genetic location for each site in the VCF file.

chr1.rMap
...
chr22.rMap

The program can also use IBD segments directly from RaPID outputs. In this case, you use the tag -O <RaPID_output_dir>.

Best, Ardalan

[catheriz]

I tried to run but always got IndexError: list index out of range, but my inputs are -i -v -g {genetic mapping file path} -p {Python version} -o {output directory}

[ardalan-n]

I uploaded a small haplotype panel including the genetic map for the sites in the panel (please see example folder). You can navigate to the Debug folder and type: ./RAFFI_v.0.1 -i ../example/vcf_files/ -v maf_0.2_chr -g ../example/genetic_maps/ -o ../example/

Best, Ardalan