Known polymorphism BED file requirements
The known polymorphism BED file indicates regions of the sequences in the custom reference FASTA file with high polymorphism (for example, SNPs, INDELs, or other variations). Ion AmpliSeq™ Designer minimizes primer overlap with these regions. This file is optional. You can upload it at the time of creating a new custom reference.
The BED format file is a tab-delimited file, with one line per region. Required fields are chrom, chromStart, and chromEnd in the first three columns. Any additional fields are ignored.
The chrom field must match one contig ID in the corresponding FASTA file. The chromStart and chromEnd fields are the zero-based half-open coordinates that indicate the region of the polymorphism in the sequence identified by the ID in the chrom field. chromStart and chromEnd are relative to the sequence of the FASTA record corresponding to the given ID.
The chrom, chromStart, and chromEnd fields must meet the following criteria.
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chromStart must be a value between 0 and length of the sequence specified by chrom−1.
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chromEnd must have a maximum value of the length of the sequence specified by chrom.
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No region should overlap any other region in the file. Merge overlapping regions into a single contiguous region.
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The BED file must have no header (for example, no "track" lines).
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The maximum files size is 2.0 GB.
