Example:

subindel -i my_paired_end_reads.SAM -g my_index -o my_result -d 300 -I 200 --paired-end

SubIndel: detect short and long indels

Usage:

subindel -i <SAM file> -g <subread index> -o <output VCF> {-d <expected fragment distance>} {-I <max indel length>} {--paired-end}

Example:

subindel -i my_paired_end_reads.SAM -g my_index -o my_result -d 300 -I 200 --paired-end