Run SVision on a pseudo-chromosome

[vegetableyu]

Hi there,
I am focusing on a specific region of the genome, so I extracted this region from the .fa file as a pseudo chromosome and got the alignment results (bam file). If I run SVision on this bam file, will I get accurate results? (Is the result of SVision affected by the chromosome?)
Best wishes.
Yu

[jiadong324]

Hi,

Just create a reference file with your fasta and made a index with samtools faidx. Use your customized fasta file as a reference for SVision.