These are chat archives for theboocock/selectionTools

31st
Mar 2015
Paloma Contreras
@PalomaUChile
Mar 31 2015 15:53

Hello, i'm trying to run the tutorial of selection tools and it isn't generating the file with iHS values. The problem is in this line of the pipeline:

Rscript ../SelectionTools/selectionTools/corescripts/multicore_iHH.R -p CEU -i CEU_genetic_dist.haps -c 2 --window 5000000 --overlap 2000000 --maf 0.0 --big_gap 0 --small_gap 0 --small_gap_penalty 0 --haplo_hh --physical_map_haps CEU_genetic_dist.pos --cores 1 --working_dir . --offset 1 --ihs

And the Error message is:
Error in scan_hh(d, big_gap = opt$big_gap, small_gap = opt$small_gap, :
unused arguments (big_gap = opt$big_gap, small_gap = opt$small_gap, small_gap_penalty = opt$small_gap_penalty, physical_positions = physical_positions)

What can I do?
murraycadzow
@murraycadzow
Mar 31 2015 19:39
Hi,
It looks like you need to install the version of rehh that comes with the pipeline because we modified it to the arguments for gap penalties
Murray