Remove annotation table dependence in VCF to FASTA script

ness-lab / mrt

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Remove annotation table dependence in VCF to FASTA script #23

Closed aays closed 4 years ago

aays commented 4 years ago

slim_vcf2fasta_chrom.py currently requires the Chlamydomonas annotation table (as well as the ANT parser) to generate reference sequence.

This could be removed by adding a separate script that generates that reference sequence as a FASTA file, after which this script would just read in that FASTA and immediately get to assigning alternate alleles based on variants in the SLiM output.

James-S-Santangelo commented 4 years ago

This will be done now since we are moving to the Drosophila genome, which has no similar annotation table.