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From: Henrikki Almusa <henrikki.almusa@he...>  20130424 08:09:53

Hi, I'm currently running both AlignmentSummaryMetrics and HsMetrics on some exome data and have slight inconsistency in results, which I'd like to understand. From website the description of values in question. === AlignmentSummaryMetrics: PF_ALIGNED_BASES: The total number of aligned bases, in all mapped PF reads, that are aligned to the reference sequence. === HsMetrics: PF_UQ_BASES_ALIGNED: The number of bases in the PF aligned reads that are mapped to a reference base. Accounts for clipping and gaps. ON_BAIT_BASES: The number of PF aligned bases that mapped to a baited region of the genome. NEAR_BAIT_BASES: The number of PF aligned bases that mapped to within a fixed interval of a baited region, but not on a baited region. OFF_BAIT_BASES: The number of PF aligned bases that mapped to neither on or near a bait. === I check the PF_ALIGNED_BASES and also ON_BAIT_BASES, NEAR_BAIT_BASES and OFF_BAIT_BASES. However the sum of the *_BAIT_BASES bases is not same as PF_ALIGNED_BASES, while it is same as PF_UQ_BASES_ALIGNED. Is the difference due to gaps and clippings as PF_ALIGNED_BASES do not mention about them (though neither does *_BAIT_BASES) or something else? Regards,  Henrikki Almusa 
From: Tim Fennell <tfennell@br...>  20130424 13:24:35

Hi Henrikki, I think the documentation for PF_UQ_BASES_ALIGNED is incorrect. If my memory serves that is the number of bases aligned to the reference from reads that are not marked as duplicated  i.e. unique (UQ) reads. It should always be <= PF_ALIGNED_BASES. Almost all metrics in the HsMetrics output after PF_UQ_ALIGNED_BASES are dealing in aligned bases from unique reads only. t On Apr 24, 2013, at 4:09 AM, Henrikki Almusa <henrikki.almusa@...> wrote: > Hi, > > I'm currently running both AlignmentSummaryMetrics and HsMetrics on some > exome data and have slight inconsistency in results, which I'd like to > understand. From website the description of values in question. > > === > AlignmentSummaryMetrics: > > PF_ALIGNED_BASES: The total number of aligned bases, in all mapped PF > reads, that are aligned to the reference sequence. > === > HsMetrics: > > PF_UQ_BASES_ALIGNED: The number of bases in the PF aligned reads that > are mapped to a reference base. Accounts for clipping and gaps. > ON_BAIT_BASES: The number of PF aligned bases that mapped to a baited > region of the genome. > NEAR_BAIT_BASES: The number of PF aligned bases that mapped to within a > fixed interval of a baited region, but not on a baited region. > OFF_BAIT_BASES: The number of PF aligned bases that mapped to neither on > or near a bait. > === > > I check the PF_ALIGNED_BASES and also ON_BAIT_BASES, NEAR_BAIT_BASES and > OFF_BAIT_BASES. However the sum of the *_BAIT_BASES bases is not same as > PF_ALIGNED_BASES, while it is same as PF_UQ_BASES_ALIGNED. > > Is the difference due to gaps and clippings as PF_ALIGNED_BASES do not > mention about them (though neither does *_BAIT_BASES) or something else? > > Regards, >  > Henrikki Almusa > >  > Try New Relic Now & We'll Send You this Cool Shirt > New Relic is the only SaaSbased application performance monitoring service > that delivers powerful full stack analytics. Optimize and monitor your > browser, app, & servers with just a few lines of code. Try New Relic > and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr > _______________________________________________ > Samtoolshelp mailing list > Samtoolshelp@... > https://lists.sourceforge.net/lists/listinfo/samtoolshelp 
From: Henrikki Almusa <henrikki.almusa@he...>  20130426 06:56:20

On 20130424 16:24, Tim Fennell wrote: > Hi Henrikki, > > I think the documentation for PF_UQ_BASES_ALIGNED is incorrect. If my memory serves that is the number of bases aligned to the reference from reads that are not marked as duplicated  i.e. unique (UQ) reads. It should always be <= PF_ALIGNED_BASES. Almost all metrics in the HsMetrics output after PF_UQ_ALIGNED_BASES are dealing in aligned bases from unique reads only. Ok, thank you. So essentially PF_ALIGNED_BASES  *_BAIT_BASES = bases of reads with mapping quality 0 (eg. nonunique reads)? > t > > On Apr 24, 2013, at 4:09 AM, Henrikki Almusa <henrikki.almusa@...> wrote: > >> Hi, >> >> I'm currently running both AlignmentSummaryMetrics and HsMetrics on some >> exome data and have slight inconsistency in results, which I'd like to >> understand. From website the description of values in question. >> >> === >> AlignmentSummaryMetrics: >> >> PF_ALIGNED_BASES: The total number of aligned bases, in all mapped PF >> reads, that are aligned to the reference sequence. >> === >> HsMetrics: >> >> PF_UQ_BASES_ALIGNED: The number of bases in the PF aligned reads that >> are mapped to a reference base. Accounts for clipping and gaps. >> ON_BAIT_BASES: The number of PF aligned bases that mapped to a baited >> region of the genome. >> NEAR_BAIT_BASES: The number of PF aligned bases that mapped to within a >> fixed interval of a baited region, but not on a baited region. >> OFF_BAIT_BASES: The number of PF aligned bases that mapped to neither on >> or near a bait. >> === >> >> I check the PF_ALIGNED_BASES and also ON_BAIT_BASES, NEAR_BAIT_BASES and >> OFF_BAIT_BASES. However the sum of the *_BAIT_BASES bases is not same as >> PF_ALIGNED_BASES, while it is same as PF_UQ_BASES_ALIGNED. >> >> Is the difference due to gaps and clippings as PF_ALIGNED_BASES do not >> mention about them (though neither does *_BAIT_BASES) or something else? >> >> Regards, >>  >> Henrikki Almusa >> >>  >> Try New Relic Now & We'll Send You this Cool Shirt >> New Relic is the only SaaSbased application performance monitoring service >> that delivers powerful full stack analytics. Optimize and monitor your >> browser, app, & servers with just a few lines of code. Try New Relic >> and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr >> _______________________________________________ >> Samtoolshelp mailing list >> Samtoolshelp@... >> https://lists.sourceforge.net/lists/listinfo/samtoolshelp >  Henrikki Almusa 
From: Tim Fennell <tfennell@br...>  20130426 10:21:09

Not quite  in this context "unique" means not marked as duplicate reads, it does not mean uniquely aligned to the genome. I.e. after running MarkDuplicates or samtools rmdup only consider the reads that are nonduplicate. t On Apr 26, 2013, at 2:56 AM, Henrikki Almusa <henrikki.almusa@...> wrote: > On 20130424 16:24, Tim Fennell wrote: >> Hi Henrikki, >> >> I think the documentation for PF_UQ_BASES_ALIGNED is incorrect. If my memory serves that is the number of bases aligned to the reference from reads that are not marked as duplicated  i.e. unique (UQ) reads. It should always be <= PF_ALIGNED_BASES. Almost all metrics in the HsMetrics output after PF_UQ_ALIGNED_BASES are dealing in aligned bases from unique reads only. > > Ok, thank you. So essentially PF_ALIGNED_BASES  *_BAIT_BASES = bases of reads with mapping quality 0 (eg. nonunique reads)? > >> t >> >> On Apr 24, 2013, at 4:09 AM, Henrikki Almusa <henrikki.almusa@...> wrote: >> >>> Hi, >>> >>> I'm currently running both AlignmentSummaryMetrics and HsMetrics on some >>> exome data and have slight inconsistency in results, which I'd like to >>> understand. From website the description of values in question. >>> >>> === >>> AlignmentSummaryMetrics: >>> >>> PF_ALIGNED_BASES: The total number of aligned bases, in all mapped PF >>> reads, that are aligned to the reference sequence. >>> === >>> HsMetrics: >>> >>> PF_UQ_BASES_ALIGNED: The number of bases in the PF aligned reads that >>> are mapped to a reference base. Accounts for clipping and gaps. >>> ON_BAIT_BASES: The number of PF aligned bases that mapped to a baited >>> region of the genome. >>> NEAR_BAIT_BASES: The number of PF aligned bases that mapped to within a >>> fixed interval of a baited region, but not on a baited region. >>> OFF_BAIT_BASES: The number of PF aligned bases that mapped to neither on >>> or near a bait. >>> === >>> >>> I check the PF_ALIGNED_BASES and also ON_BAIT_BASES, NEAR_BAIT_BASES and >>> OFF_BAIT_BASES. However the sum of the *_BAIT_BASES bases is not same as >>> PF_ALIGNED_BASES, while it is same as PF_UQ_BASES_ALIGNED. >>> >>> Is the difference due to gaps and clippings as PF_ALIGNED_BASES do not >>> mention about them (though neither does *_BAIT_BASES) or something else? >>> >>> Regards, >>>  >>> Henrikki Almusa >>> >>>  >>> Try New Relic Now & We'll Send You this Cool Shirt >>> New Relic is the only SaaSbased application performance monitoring service >>> that delivers powerful full stack analytics. Optimize and monitor your >>> browser, app, & servers with just a few lines of code. Try New Relic >>> and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr >>> _______________________________________________ >>> Samtoolshelp mailing list >>> Samtoolshelp@... >>> https://lists.sourceforge.net/lists/listinfo/samtoolshelp >> > > >  > Henrikki Almusa 
From: Henrikki Almusa <henrikki.almusa@he...>  20130426 10:25:27

On 20130426 13:21, Tim Fennell wrote: > Not quite  in this context "unique" means not marked as duplicate reads, it does not mean uniquely aligned to the genome. I.e. after running MarkDuplicates or samtools rmdup only consider the reads that are nonduplicate. Then there is something odd. Since the bam has had the duplicate reads removed by MarkDuplicates. > t > > On Apr 26, 2013, at 2:56 AM, Henrikki Almusa <henrikki.almusa@...> wrote: > >> On 20130424 16:24, Tim Fennell wrote: >>> Hi Henrikki, >>> >>> I think the documentation for PF_UQ_BASES_ALIGNED is incorrect. If my memory serves that is the number of bases aligned to the reference from reads that are not marked as duplicated  i.e. unique (UQ) reads. It should always be <= PF_ALIGNED_BASES. Almost all metrics in the HsMetrics output after PF_UQ_ALIGNED_BASES are dealing in aligned bases from unique reads only. >> >> Ok, thank you. So essentially PF_ALIGNED_BASES  *_BAIT_BASES = bases of reads with mapping quality 0 (eg. nonunique reads)? >> >>> t >>> >>> On Apr 24, 2013, at 4:09 AM, Henrikki Almusa <henrikki.almusa@...> wrote: >>> >>>> Hi, >>>> >>>> I'm currently running both AlignmentSummaryMetrics and HsMetrics on some >>>> exome data and have slight inconsistency in results, which I'd like to >>>> understand. From website the description of values in question. >>>> >>>> === >>>> AlignmentSummaryMetrics: >>>> >>>> PF_ALIGNED_BASES: The total number of aligned bases, in all mapped PF >>>> reads, that are aligned to the reference sequence. >>>> === >>>> HsMetrics: >>>> >>>> PF_UQ_BASES_ALIGNED: The number of bases in the PF aligned reads that >>>> are mapped to a reference base. Accounts for clipping and gaps. >>>> ON_BAIT_BASES: The number of PF aligned bases that mapped to a baited >>>> region of the genome. >>>> NEAR_BAIT_BASES: The number of PF aligned bases that mapped to within a >>>> fixed interval of a baited region, but not on a baited region. >>>> OFF_BAIT_BASES: The number of PF aligned bases that mapped to neither on >>>> or near a bait. >>>> === >>>> >>>> I check the PF_ALIGNED_BASES and also ON_BAIT_BASES, NEAR_BAIT_BASES and >>>> OFF_BAIT_BASES. However the sum of the *_BAIT_BASES bases is not same as >>>> PF_ALIGNED_BASES, while it is same as PF_UQ_BASES_ALIGNED. >>>> >>>> Is the difference due to gaps and clippings as PF_ALIGNED_BASES do not >>>> mention about them (though neither does *_BAIT_BASES) or something else? >>>> >>>> Regards, >>>>  >>>> Henrikki Almusa >>>> >>>>  >>>> Try New Relic Now & We'll Send You this Cool Shirt >>>> New Relic is the only SaaSbased application performance monitoring service >>>> that delivers powerful full stack analytics. Optimize and monitor your >>>> browser, app, & servers with just a few lines of code. Try New Relic >>>> and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr >>>> _______________________________________________ >>>> Samtoolshelp mailing list >>>> Samtoolshelp@... >>>> https://lists.sourceforge.net/lists/listinfo/samtoolshelp >>> >> >> >>  >> Henrikki Almusa >  Henrikki Almusa 
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