AdamaJava Wiki
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The [qMito] summarise mode produces mitochondrial sequencing summary reports from BAM files.
Usage:
usage: java -jar qmito-0.2pre.jar summarise -i <BAM> -o <output> --log <log_file> Option Description ------ ----------- -i,--input <input BAM> Input BAM file -o,--output <count file> Output file --log <log file> Log file --thread <thread number> (Optional) number of execution threads (default=2)
The summarise mode only works on single BAMs so if you have tumour/normal pairs, or families or other collections of related BAM files that you may wish to analyse jointly, you will still need to run the qMito summarise mode independently on each of the BAMs.
Design
java -jar -Xms5g -Xmx5g qmito-0.1pre.jar \ -i $tumourBAM \ -o ${tumourBAM}.qmito.tsv \ --log ${tumourBAM}.qmito.log
Output is a tab-separated plain-text file with unix line endings. The format is that each position in the mitochondrial genome is a row and the columns are the various parameters collected at each position.
#position A_forward C_forward G_forward T_forward … 1 7 95 0 0 2 93 0 0 0 3 0 0 107 2 4 0 8 96 1 ...