Depending on a) whether you’re dealing with human, another diploid organism or
something else and b) what kind of data you have (wgs, exome, other) you might
start with Heng’s CHM1 paper as an interesting read:
http://arxiv.org/pdf/1404.0929.pdf
-t
On Oct 8, 2014, at 9:58 AM, mehar <[email protected]> wrote:
> Hi all,
>
> Knowing the fact that filtering variants manually, using thresholds on
> quality values, is subject to all sorts of caveats i am writing this to seek
> some suggestion for hard filtering variants as it is better than nothing.
>
> Could someone provide generic recommendations using samtools that should at
> least provide a starting point to analyse the data.
>
> Awaiting for suggestions!!
>
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