From 06edaa4704f6fcfdca2ab1b7a78bbdc9ab359f8b Mon Sep 17 00:00:00 2001 From: verku Date: Thu, 5 Oct 2023 17:11:30 +0200 Subject: [PATCH] Update documentation --- config/config.yaml | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/config/config.yaml b/config/config.yaml index 3844bce..cf28bf3 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -27,13 +27,12 @@ ref_path: "" # Relative path (from the main pipeline directory) to file listing # scaffolds/contigs linked to sex chromosomes (one scaffold/contig # name per line). -# If provided, the listed scaffolds/contigs are excluded from mlRho -# analyses (but see below how to run mlRho for autosomes and sex -# chromosomes separately from each other) and from the merged BCF file -# that is used for PCA, ROH, snpEff and GERP analyses. +# Is used to create BED files to run mlRho separately for autosomes +# and sex chromosomes or exclusively for autosomes, and/or to create +# autosome-only BCF files for PCA, ROH, snpEff and GERP analyses. # Can also be used to specify any other contigs/scaffolds, e.g. -# unplaced or short scaffolds, for removal from the mlRho analysis -# and BCF file. +# unplaced or short scaffolds, for removal from mlRho analysis +# and BCF files. # Leave empty ("") if identity of sex chromosomes is unknown and/or # if the pipeline should be run on all scaffolds/contigs of the genome. sexchromosomes: "" # for example, "config/chrX_candidate_scaffolds.txt"