Hi.
Follow-up to my previous email, vcftools is used to filter based on
different quality annotations as shown below:
Usage: vcfutils.pl varFilter [options] <in.vcf>
-Q INT minimum RMS mapping quality for SNPs [10]
-d INT minimum read depth [2]
-D INT maximum read depth [10000000]
-a INT minimum number of alternate bases [2]
-w INT SNP within INT bp around a gap to be filtered [3]
-W INT window size for filtering adjacent gaps [10]
-1 FLOAT min P-value for strand bias (given PV4) [0.0001]
-2 FLOAT min P-value for baseQ bias [1e-100]
-3 FLOAT min P-value for mapQ bias [0]
-4 FLOAT min P-value for end distance bias [0.0001]
-e FLOAT min P-value for HWE (plus F<0) [0.0001]
-p print filtered variants
Any suggestions on which of these parameters and thresholds to use is
what i am looking as a starting point.
On 09/10/14 13:13, 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 <[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!!
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