Re: [maq-help] SNP filtering and calling

[Olivier H. <oh...@sc...>]

Thanks for you answer, however, I am not sure it clears up  
everything. My question was also : when do you call a SNP ? what is  
the minimum frequency of an alternate base to be considered a true  
variant : 0.1 ? 0.2 ?

Is there a way to play on the coverage for SNP calling or do I have  
to parse the pileup output to do that ?

best,

Olivier



On Nov 28, 2007, at 1:36 AM, Heng Li wrote:

> Dear Olivier,
>
> Thanks for the feed back. maq-0.6.2 and maq-0.6.1 use different  
> rules in filtering SNPs. In maq-0.6.2, the following rules are used  
> to get cns.final.snp:
>
> "After mapping and consensus base calling, we filtered the SNPs  
> based on
> four rules: [i') discard SNPs in 3bp-flanking regions beside potential
> indels;] i) discard SNPs covered by three or fewer reads; ii) discard
> SNPs covered by no read with a mapping quality higher than 40; iii) in
> any 10bp window, if there are 3 or more SNPs, discard them all; and  
> iv)
> discard SNPs with quality smaller than 40."
>
> In some cases, you can reduce the threshold on the quality of SNP  
> (rule iv), but the false positive may increase a little. For single- 
> end reads, you may also try:
>
> maq.pl SNPfilter -a cns.snp > cns.filtered.snp
>
> This command will invoke an alternative filter which is with  
> similar aim but slightly different from rule ii).
>
> As for the last column in *.snp, you can ignore them. Even I do not  
> use them any longer. Maybe I should remove that column some day.
>
> Hope this helps.
>
> Cheers,
>
> Heng
>
>
> On 27 Nov 2007, at 22:20, Olivier Harismendy wrote:
>
>> Hi,
>>
>> I have question about the cns.final.snp output file from maq.pl  
>> easyrun.
>>
>> What are the filters applied to the SNPs (depth/repeats/quality) ?  
>> Is there a way to play with the parameters ?
>>
>> In the output, the last column (quality difference between strong  
>> and weak allele) doesn't make sense to me as the values go from  
>> -124 to 124. Can you explain a little ?
>>
>> thanks for your answer.
>>
>> Olivier
>>
>>
>>
>>
>> --------------------------------------------------------------------- 
>> ----
>> This SF.net email is sponsored by: Microsoft
>> Defy all challenges. Microsoft(R) Visual Studio 2005.
>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ 
>> _______________________________________________
>> maq-help mailing list
>> maq...@li...
>> https://lists.sourceforge.net/lists/listinfo/maq-help
>