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Info

Currently only BAM files are supported. The BAM files used as input for the Flux Capacitor should be sorted by genomic position and should have the index placed in the same folder. The index is needed to access every locus indipendently, without the need to sequentially read the whole file.

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Samtools can be used to pre-process the file for the Flux capacitor:

Sort the BAM file:

Code Block
samtools sort file.bam file_sorted

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Create the index:

to create the index, the BAM file has to be sorted by genomic position. Then you could run:

Code Block
samtools index file.bam

 

Multiple alignments:
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ID:1:2:3    385    1    135712    1    76M    =    135833    122    CTACCAGGGCCGCTGGGAGCTGGGCAGGAGCTGAGTCCAAAGACGTTGTTGGGACCTGGAGTCGGGCCAGAGTCCG
@@@FFFFFHDHFFGGIIGHGIIJIIIFGFEEFHECDHGCBHIGIIDCACA(;5?@?ED@;?;C?688;?(82::>?
ID:1:2:3    321    1    135833    1    76M    =    135712    -12    CCGGGAGGCTGCAAGTGGGTCTGAGAGGCCAACTTGAGGAGGCCTGGCCTCTGCCTCCCACATTGCCCAGCTGTTC    
@@@FFADFGHHHHGIGHGCGGIIIGGHCHHIJJJIJIGD?FDGHIGHIIIIJAHGHHHGFD?DECCCCE?DCC>@C
ID:1:2:3    385    1    662078    1    76M    =    662199    122    CTACCAGGGCCGCTGGGAGCTGGGCAGGAGCTGAGTCCAAAGACGTTGTTGGGACCTGGAGTCGGGCCAGAGTCCG    
@@@FFFFFHDHFFGGIIGHGIIJIIIFGFEEFHECDHGCBHIGIIDCACA(;5?@?ED@;?;C?688;?(82::>?
ID:1:2:3    321    1    662199    1    76M    =    662078    -12    CCGGGAGGCTGCAAGTGGGTCTGAGAGGCCAACTTGAGGAGGCCTGGCCTCTGCCTCCCACATTGCCCAGCTGTTC    
@@@FFADFGHHHHGIGHGCGGIIIGGHCHHIJJJIJIGD?FDGHIGHIIIIJAHGHHHGFD?DECCCCE?DCC>@C