GermLineUtility
We have created some script utilities for converting between data formats; the source code is available below. All scripts can
be compiled using g++ [script file] -o [output name].
Commands:
1)bash run.sh [ped file] [map file] [output]
-Pipeline for phasing PLINK format data with BEAGLE and processing in GERMLINE. README for detailed usage.
Source
phasing_pipeline.tgz
2)./ped_to_bgl [ped file] [map file] > out.bgl
-Takes PLINK .PED and .MAP file as input and converts into BEAGLE format to be phased.
Source
ped_to_bgl.cpp
3)./bgl_to_ped [beagle file] [fam file] > out.ped
-Takes BEAGLE-format file and PLINK .FAM file and converts into PLINK .PED format to be processed by GERMLINE.
Source
bgl_to_ped.cpp
