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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. |
Using samtools to fullfill BAm file requirements:
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Sort the BAM file:
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samtools sort file.bam file_sorted |
Creating the index:
to create the index, the BAM file has to be sorted by genomic position. Then you could run:
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