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Profiles ancient DNA samples for typical damage patterns, producing a variety of plots and statistics.
Usage: DamageProfiler [-h] [-v] [-i <INPUT>] [-o <OUTPUT>] [-r <REFERENCE>] [-t <THRESHOLD>] [-s <SPECIES>] [-sf <SPECIES FILE>] [-l <LENGTH>] [-title <TITLE>] [-yaxis_dp_max <MAX_VALUE>] [-color_c_t <COLOR_C_T>] [-color_g_a <COLOR_G_A>] [-color_insertions <COLOR_C_T>] [-color_deletions <COLOR_DELETIONS>] [-color_other <COLOR_OTHER>] [-only_merged] [-sslib]
DamageProfiler [-h] [-v] [-i <INPUT>] [-o <OUTPUT>] [-r <REFERENCE>] [-t <THRESHOLD>] [-s <SPECIES>] [-sf <SPECIES FILE>] [-l <LENGTH>] [-title <TITLE>] [-yaxis_dp_max <MAX_VALUE>] [-color_c_t <COLOR_C_T>] [-color_g_a <COLOR_G_A>] [-color_insertions <COLOR_C_T>] [-color_deletions <COLOR_DELETIONS>] [-color_other <COLOR_OTHER>] [-only_merged] [-sslib]
Example grave command:
damageprofiler -Xms2g -Xmx\${MAX_HEAP_GB}g -i ${meta.id}.dedup.bam -r ${reference_fasta} -o ${meta.id}_pmd -t 20 -l 100 -yaxis_dp_max 0.3