Converting .delta file from NUCMER to format accepted by IGV? (.bam/.vcf)

Question

[Joanna]

Hi!

I'm currently having my first go at bioinformatics analysis of WGS data:) I used Nucmer to align my assembled sequence to a reference sequence and I would like to view the alignment in IGV (intergative genomics viewer), however it will only accept .bam/.vcf files and Nucmer output format is a .delta file. Is there a way to convert the delta file into sam/vcf format? Or alternatively, is there a software that allows to view/annotate alignments in .delta format?

[GenoMax]

Have you seen the dnadiff utilities (LINK) that can extract useful info from .delta files?

[Joanna]

Thank you, I have not seen this! I originally extracted SNPs with mummer and was trying to map them back to my annotated reference sequence but it seems like for this I might have to use a different alignment software that will generate a .bam file, like suggested :)

[WouterDeCoster]

I would suggest using minimap2 or LRA for this task, which also will generate an output in BAM format. I do not think that Nucmer is still the most ideal solution for the alignment of contigs to a reference.