These are also one of the primary targets for aligners that clip
low-quality tails.


On Mon, Jan 27, 2014 at 2:01 PM, christopherlhartl@gmail.com <
christopherlhartl@gmail.com> wrote:

> Q2 is a legacy value; it's effectively Illumina's garbage value; they tend
> to be bad bases even after recalibration. Q2 is what the machine produces
> when it's read through a nucleotide repeat and has no real idea what the
> bases are. See below: all the faint bases are Q2.
> [image: Inline image 1]
>
>
> On Mon, Jan 27, 2014 at 1:54 PM, Matt Massie <notifications@github.com>wrote:
>
>> In
>> adam-core/src/main/scala/edu/berkeley/cs/amplab/adam/rdd/recalibration/ReadCovariates.scala:
>>
>> > @@ -28,27 +28,35 @@ object ReadCovariates {
>> >  }
>> >
>> >  class ReadCovariates(val read: RichADAMRecord, qualByRG: QualByRG, covars: List[StandardCovariate],
>> > -                     val dbSNP: SnpTable) extends Iterator[BaseCovariates] with Serializable {
>> > +                     val dbSNP: SnpTable, val minQuality:Int = 2) extends Iterator[BaseCovariates] with Serializable {
>>
>> I think Phred 2 is P=0.63
>>
>>
>> https://www.google.com/search?q=10+%5E+(-2%2F10)&oq=10+%5E+(-2%2F10)&aqs=chrome..69i57j0j69i64l2.7131j0j7&sourceid=chrome&espv=210&es_sm=119&ie=UTF-8
>> )
>>
>> —
>> Reply to this email directly or view it on GitHub<https://github.com/bigdatagenomics/adam/pull/60/files#r9200596>
>> .
>>
>
>