Hi Mehar,
there are some tips on this wiki page
https://github.com/samtools/bcftools/wiki/HOWTOs
Petr
On 9 Oct 2014, at 11:13, mehar wrote:
> Hi,
>
> Thank you for your response.
>
> I am dealing with dog genome which is a diploid organism and as big as human
> genome. We have both WGS and WES data, and struck with huge amount of
> variants in both the datasets and would like to do hard filtering to start
> off.
>
> In the paper "http://arxiv.org/pdf/1404.0929.pdf"; certain filters which are
> applicable to a set of variant callers are choosen and applied to their
> datasets. However, any thresholds were not mentioned.
>
> Would be valuable if someone can cite filters to be applied specific to
> samtools.
>
> Regards
> Mehar
> On 08/10/14 18:20, Tim Fennell wrote:
>> 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 <meharji.arumi...@helsinki.fi> 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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