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

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

indels structural variations whole genome mouse
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updated by d-cameron d-cameron • written by Ankit Ankit

2 answers

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

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written by Pierre Lindenbaum Pierre Lindenbaum

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

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written by Ankit Ankit

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.

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written by d-cameron d-cameron

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