Hey Siva,
based upon my reading reads are ignored in *CalculateHsMetrics* if they are
one of secondary, supplemental, fail vendor QC checks, marked as
duplicates, zero mapping quality, or unmapped. These are hard-coded at
the moment.
The relevant code is in the "*acceptRecord*" method in Picard:
https://github.com/broadinstitute/picard/blob/master/src/java/picard/analysis/directed/TargetMetricsCollector.java
If you have a case that is not in one of the list above, could you please
submit a test case for us to look at?
Nils
On Mon, Sep 15, 2014 at 3:02 PM, Gowrisankar, Sivakumar <
[email protected]> wrote:
> Hi All
>
>
>
> I target a highly homologous target region of about 300 Kb. I have an
> bwa-aligned BAM file that is not marked for duplicates. When I use Picard
> to CollectHsMetrics, I find that about 15% of the region is not covered
> (using PCT_TARGET_BASES_2X). As far as I know all my regions are covered,
> which I checked this with complementary tools such as CallableLoci from
> GATK.
>
>
>
> My question is does Picard ignore Low/Zero MQ reads while estimating
> different metrics?
>
>
>
> Thanks
>
> Siva
>
>
>
>
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