Trying to check plasmid alignment

Question

[gracie]

Hi,

I got a plasmid for overexpression but before going further I would like to check the everything is correct, with no significant insertions or deletions. I got sorted .bam files and .genome file for the vector and uploaded to the igv. Although I could detect SNPs and deletions, I couldnot figure out how to detect insertions? I have changed the color alignment option to insert size but still I don't know how to interpret the results. Is there any way to generate a report showing all insertions, deletions and SNPs with igv or with some other tool?

Thanks in advance

[Pierre Lindenbaum]

how about 'just' looking at a vcf called by samtools ?

[gracie]

Thanks, it worked .