Lumpy applicability

[anleopa]

Hi, I would like to know if lumpy can be also used to call germline and short variants, or its use for such situations is not recommended.

[ryanlayer]

Germline, for sure. But how short are you interested in?

On Tue, Dec 14, 2021 at 9:05 AM anleopa @.***> wrote:

Hi, I would like to know if lumpy can be also used to call germline and short variants, or its use for such situations is not recommended.

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[anleopa]

I was thinking about SNPs and small indels

[williambrandler]

@anleopa I have used lumpy to good effect for structural variation detection in paired-end sequencing data, where the break points create split or discordant reads. Manta is also a good tool for this (https://github.com/Illumina/manta).

Manta does not include read depth, so will miss copy number variants that are mediated by non-allelic homologous recombination. For those you want a segmentation algorithm that accounts for read depth.

You can combine the results from multiple copy number and structural variant algorithms and genotype them with an algorithm like SV2 (https://github.com/dantaki/SV2)

For SNPs and indels, deep variant is becoming the gold standard (https://github.com/google/deepvariant), consider also freebayes and gatk