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.
For the SAM format, the Flux Capacitor needs the input file to be indexed. The index is needed to access every locus indipendently, without the need to sequentially read the whole file. For this reason only BAM files are supported.
The BAM file used as input for the Flux Capacitor should be sorted by genomic position and indexed. The index file has to be placed in the same folder as the BAM file.
Example.
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
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.
The following example shows the required representation for 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
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 files to be used as the input of the Flux Capacitor.
1.Convert SAM file to BAM file:
samtools view -Sb file.sam > file.bam
2.Sort the BAM file by genomic position:
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:
samtools index file_sorted.bam
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