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 <[email protected]
<mailto:[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!!
------------------------------------------------------------------------------
Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer
Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports
Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper
Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk_______________________________________________
Samtools-help mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/samtools-help
------------------------------------------------------------------------------
Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer
Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports
Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper
Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk
_______________________________________________
Samtools-help mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/samtools-help
