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Info

The BAM file cannot contain multiple alignments per entry/line ("compact format" NOT allowed).

Example.

The following example shows a valid mapped read-pair in SAM format:

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ID:1:2:3    129    chr1    127926    1    75M    =    128047    122    CTACCAGGGCCGCTGGGAGCTGGGCAGGAGCTGAGTCCAAAGACGTTGTTGGGACCTGGAGTCGGGCCAGAGTCCG    
@@@FFFFFHDHFFGGIIGHGIIJIIIFGFEEFHECDHGCBHIGIIDCACA(;5?@?ED@;?;C?688;?(82::>?
ID:1:2:3    65    chr1    128047    1    75M    =    127926    -122    CCGGGAGGCTGCAAGTGGGTCTGAGAGGCCAACTTGAGGAGGCCTGGCCTCTGCCTCCCACATTGCCCAGCTGTTC    
@@@FFADFGHHHHGIGHGCGGIIIGGHCHHIJJJIJIGD?FDGHIGHIIIIJAHGHHHGFD?DECCCCE?DCC>@C

Multiple alignments.

The Flux Capacitor supports input files in SAM format containing multiple mappings. These alignments should be represented in an extended format, that is each line contains a single alignment and flag 256 have to be used to specify that the alignment is secondary. The usage of optional fields for representing multiple alignments on a single line is currently not supported.

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ID:1:2:3    385    chr1    135712    1    75M    =    135833    122    CTACCAGGGCCGCTGGGAGCTGGGCAGGAGCTGAGTCCAAAGACGTTGTTGGGACCTGGAGTCGGGCCAGAGTCCG
@@@FFFFFHDHFFGGIIGHGIIJIIIFGFEEFHECDHGCBHIGIIDCACA(;5?@?ED@;?;C?688;?(82::>?
ID:1:2:3    321    chr1    135833    1    75M    =    135712    -122    CCGGGAGGCTGCAAGTGGGTCTGAGAGGCCAACTTGAGGAGGCCTGGCCTCTGCCTCCCACATTGCCCAGCTGTTC    
@@@FFADFGHHHHGIGHGCGGIIIGGHCHHIJJJIJIGD?FDGHIGHIIIIJAHGHHHGFD?DECCCCE?DCC>@C
ID:1:2:3    385    chr1    662078    1    75M    =    662199    122    CTACCAGGGCCGCTGGGAGCTGGGCAGGAGCTGAGTCCAAAGACGTTGTTGGGACCTGGAGTCGGGCCAGAGTCCG    
@@@FFFFFHDHFFGGIIGHGIIJIIIFGFEEFHECDHGCBHIGIIDCACA(;5?@?ED@;?;C?688;?(82::>?
ID:1:2:3    321    chr1    662199    1    75M    =    662078    -122    CCGGGAGGCTGCAAGTGGGTCTGAGAGGCCAACTTGAGGAGGCCTGGCCTCTGCCTCCCACATTGCCCAGCTGTTC    
@@@FFADFGHHHHGIGHGCGGIIIGGHCHHIJJJIJIGD?FDGHIGHIIIIJAHGHHHGFD?DECCCCE?DCC>@C

Using SAM tools to pre-process input files for the Flux Capacitor.

SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Please see more here. These tools can be used to prepare a BAM file which can be used as the input file for the Flux Capacitor.

1.Convert SAM file to BAM file:
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samtools view -Sb file.sam > file.bam
2.Sort the BAM file:
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samtools sort file.bam file_sorted
3.Create the index:

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

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