MAPPING_KMERS

MAPPING_KMERS section in PARAMS can optionally be used to align kmers to a genomic reference. It could give a idea of selected regions in a genome.

PARAMS:
   MAPPING_KMERS:
      REF: "reference.fasta"
      MODE : bwa-aln
      INDEX_OPTIONS: ""
      OPTIONS : "-n 0.04"
      FILTER_FLAG : 4
      FILTER_QUAL : 10

Use a reference file in the REF section.

Parameter MODE using bwa-aln or bwa-mem2

Set up the INDEX_OPTIONS according to the MODE you have chosen.

If bwa-mem2 leaf empty

If bwa-aln “-a bwtsw” or “”

Set options according of chosen mapper in the OPTIONS key.

If bwa-mem2 default parameters -A 1 -B 4;

If bwa-aln -n 0.04

Obtained bam could be filtered using FILTER_FLAG (-F 4 by default) and FILTER_QUAL (mapq>10 by defaut) params.