Question: primer design tool suggestions
1
gravatar for novicebioinforesearcher
2.9 years ago by

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?

Thanks.

dna structural variant primer • 1.1k views
ADD COMMENTlink written 2.9 years ago by novicebioinforesearcher50
2

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.

ADD REPLYlink written 2.9 years ago by Pierre Lindenbaum127k

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?

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by novicebioinforesearcher50

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.

ADD REPLYlink written 2.9 years ago by trausch1.4k

i am aware of primer3, what I am looking for is a tool which would take list of positions and generate primers against them.

ADD REPLYlink written 2.9 years ago by novicebioinforesearcher50
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