Can I use MosaicForecast for ~30X WGS dataset?

[changhan1110]

Hi,

I used DeepMosaic to detect mosaic SNVs from low-depth WGS data, because it supports low-depth samples, but DM does not call mosaic INDELs. I would like to detect mosaic INDELs from ~30X WGS dataset of normal people.

Do you recommend me to use this tool for the purpose? (MF paper does not show that MF does fit the low-depth data.)

Thanks, Changhan

[douym]

Hi,

I used DeepMosaic to detect mosaic SNVs from low-depth WGS data, because it supports low-depth samples, but DM does not call mosaic INDELs. I would like to detect mosaic INDELs from ~30X WGS dataset of normal people.

Do you recommend me to use this tool for the purpose? (MF paper does not show that MF does fit the low-depth data.)

Thanks, Changhan

Hi Changhan,

I would not highly recommend using shallow WGS data from non-cancer samples to call somatic mutations, since somatic mutations in normal samples typically have relatively low VAF and presumably you would expect to have high False-negative rate. However, for some samples expected to have high probability of clonal expansion (i.e., hematopoetic cells in aged people), you could give a try.

Best,

Y.