Tools to call Large indels/structural variations in whole genome BAM data of mouse strain?

Question

[Ankit]

Hi everyone,

I would like to know if there are tools to call large indels/structural variations in data of mouse strain.

I have bam files obtained online from ftp://ftp-mouse.sanger.ac.uk/REL-1905-BAM/. The data was aligned to GRCm38. For reference genome I have fasta file. I specifically want to detect large deletions present in mouse strain.

Please help.

Thanks

Answer 1

[Pierre Lindenbaum]

indexcov : https://github.com/brentp/goleft/tree/master/indexcov

[Ankit]

Thanks for help. Any other alternative software. I could not understand the package well.

Answer 2

[d-cameron]

Two recent SV benchmarking papers are:

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1720-5

and

https://www.nature.com/articles/s41467-019-11146-4

GRIDSS and manta are currently the best performing short read breakpoint callers, not sure about what the best-in-class CNV caller is.