Sequence centering around non-variant position

Help & Support
1

Hi,

Is it possible to centre the sequence around a different position other than the variant position?

For e.g., the sequence is centered at position 109441014 and the SNP variant position is at 109433374 and i want to calculate the score across 109448655 to 109477359.

variant = genome.Variant(
            chromosome=str(vcf_row['CHR']),
            position=int(vcf_row['POS']),
            reference_bases=str(vcf_row['REF']),
            alternate_bases=str(vcf_row['ALT']),
            name=vcf_row['ID']
        )
sequence_length = 1048576
sequence_centering = int(str(vcf_row['seq_pos']))
default_interval = variant.reference_interval
interval = type(default_interval)(
                chromosome=default_interval.chromosome,
                start=sequence_centering - (sequence_length // 2),
                end=sequence_centering + (sequence_length // 2),
                strand=default_interval.strand,
                name=default_interval.name)

is it ok to do something like this ?

Thanks, Sanjana

2

This should work so long as the variant is within the interval region, though we’ve not thoroughly evaluated the model’s performance for this use-case (there may well be some distal effects if the variant is at the edges of the window).