qMito summarise

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

• read in a single BAM
• use qbamfilter to only keep read pairss we want: and( or(RNAME == 'chrM', RNEXT == 'chrM'), not 2ndary alignment, not fail vendor check)
• note that DUPs and unmapped reads are OK which means the filter should pull out pairs where one or both reads mapped to the mitochondrial sequence
• write a report with the same params as Felicity's pileup (approx 40 params) but we want to write it to a TSV file, not eh HDF5 format used by qpileup.

Example

 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
...