molgenis/molgenis-imputation — pull request #11 by kantale (2013-12-19 15:56:00+00:00)
Title: check comments

Fix issues:

To come back to our points:
* When running with "--action liftover" the script detects any file with chr in the file name in the study directory and uses it as input and writes files to be used for phasing in build37.
We already had data in build37, so no liftover was required. When running the python script with "--action phase" the script however assumes that data is named like chr*.ped, which is the output filename convention from the liftover. Our input study data wasn't named like this, so the phasing didn't work. Solution would be to mention this in the manual or even better, let this step also search through a directory and detect any filenames containing "chr" automatically, like it does in the liftover step.

* We didn't use the default commandline as specified in the manual, we added some additional parameters. We had PED/MAP study data, but somehow the python script didn't detect it was ped/map data.
The first check in the python script checks for BED/BIM format and it somehow ran into this loop, thinking our study data was binary, which it wasn't. We now changed the value in the script to PED, instead of BED, which solved our problem (dirty hack). If you need more detailed information on how to reproduce this problem please let me know.

* Our reference panel already consisted of VCF, haps en legend files, since we used GoNL release 4 for testing. During "--action imputation"" the pipeline requires *.vcf.gz files to be in the reference directory. The pipeline then gzips our VCF files, but also regenerates the haps en legend files. This creates new files by prepending something like pyp.haps en pyp.legend, which is not needed because the haps en legend files already exist. This also makes the generation time of these gzipped VCF file much longer. Can this be fixed somehow?