toolkit to process routine operation on gff3, vcf and fasta files
Project description
ANVAGE
ANnotation Variants GEnome is a toolkit software to perform routine operations that involve VCF, GFF3 and FASTA genome files.
usage
anvage select --vcf tests/data/sample.vcf \
--genome tests/data/genome.fasta \
--annotation tests/data/genome.gff3 \
--selectionAnnotationType CDS \
--output_prefix res
anvage synonymous --vcf tests/data/sample.vcf \
--genome tests/data/genome.fasta \
--annotation tests/data/genome.gff3 \
--output_prefix res
anvage flank --vcf tests/data/sample.vcf \
--genome tests/data/genome.fasta \
--windowsSize 25 \
--output_prefix res
https://github.com/laurabenestan/BLAST/blob/master/flanking_sequence.py
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