Kmers module

KMERS_GWAS module decompose reads into kmers and create a binary table of presence/absence of kmers. This table can be filter to use only most informative kmers into the populations. PLINK format outfile are obtained in this module.

PARAMS:
   KMERS_MODULE:
      KMER_SIZE : 31
      MAC : 2
      P : 0.2
      MAF : 0.05
      B : 1000000 # nb kmers in each bed file
      SPLIT_LIST_SIZE : 100000
      MIN_LIST_SIZE : 50000
      SAMPLES_FILE: "samples.txt"

Type	Description	Default Value
KMER_SIZE	Length of kmers (should be between 15-31)	31
MAC	Minor allele count (min allowed appearance of a kmer)	2
P	Minimum percent of appearance in each strand form	0.2
MAF	Minimum allele frequency	0.05
B	Number of kmers in each bed file	1000000
SPLIT_LIST_SIZE	Number of kmers by bed file	100000
MIN_LIST_SIZE	Minimal number of kmers allowed in the smaller bed file after splitting	50000

Note

if you active KMERS_MODULE and no active PCADAPT and LFMM, iKISS calculate occurrences of presence and absence of kmers into the populations using the whole of kmers and groups given by user into the SAMPLES_FILE. If MAPPING and INTERSECT are also activated you can check occurrences found into chosen features (genes). Check the ‘go away in global mode’ section.