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The BAM file cannot contain multiple alignments per entry/line ("compact format" NOT allowed). |
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 |
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 |
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.
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samtools view -Sb file.sam > file.bam |
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samtools sort file.bam file_sorted |
to create the index, the BAM file has to be sorted by genomic position. Then you could run:
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