Is there any tool/script that would take a vcf or bedpe/bed file generated using a structural variant caller eg, manta from illumina and design primers to validate them?
extract the start-end from your variants, extends this interval, get the fasta sequence with samtools faidx , convert this fasta sequence to primer3 using awk, and pipe into primer3.
or take programming/bioinformatics course (or buy biostars bioinfo handbook) before venturing out to perform steps mentioned :) thanks will see how it goes , so the bedpe file i have has co ordinates for two breakpoints how do I address this?
Local primer candidates from primer3 we usually check in addition genome-wide for uniqueness using BLAST or BLAT because SVs are often embedded in repeats.
i am aware of primer3, what I am looking for is a tool which would take list of positions and generate primers against them.