SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. Further information about it can be read in the SAM format specifications document.
The following example shows a valid mapped read-pair in SAM format:
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
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.
Samtools can be used to pre-process the BAM file for the Flux capacitor:
Sort the BAM file:
samtools sort file.bam file_sorted
Create the index:
to create the index, the BAM file has to be sorted by genomic position. Then you could run:
samtools index file.bam
Multiple alignments:
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
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