[Dongliang Ge]

Dongling,
Will SVA provide quantitative estimation of reads in mutated regoin? IS it mainly for SNPs or it can also detect rearrangement please?

Hi,

For variant or given genomic regions, yes SVA will provide summary of read depth (and other quality measures for example SNP quality).

SVA can read SNV, indel, and large SV calls, together with their quality measures. However, I need to note that SVA itself is not a variant caller. It reads variant calls (generated by for example SAMTools), and annotate and visualize them.

All the best,

Dongliang

[iandbear]

Hi Dongliang,
Do you have any suggestion on how to detect rearrangement using whole genome sequencing data? Any tools? Thanks!

Hi,

For variant or given genomic regions, yes SVA will provide summary of read depth (and other quality measures for example SNP quality).

SVA can read SNV, indel, and large SV calls, together with their quality measures. However, I need to note that SVA itself is not a variant caller. It reads variant calls (generated by for example SAMTools), and annotate and visualize them.

All the best,

Dongliang