Hi Andreas, On Fri, 2014-10-17 at 18:53 +0800, Andreas Wilm wrote: > Hi Petr, > > thanks for your reply. With -x in samtools 1.0 some of the previously > listed BAQ values change / get reduced and one 0 value is now at 36, > but the one of interest (i.e the alternate C) still receives a zero: > > samtools 1.0 > chrX 46918110 G 21 cc,c,,,,,.c.,,..,..., 4 0 36 38 38 38 37 34 34 77 > 37 75 35 0 73 37 0 32 34 29 0 > samtools 1.0 > with -x > chrX 46918110 G 21 cc,c,,,,,.c.,,..,..., 4 0 36 38 38 38 37 34 34 38 > 37 39 35 39 38 37 35 32 34 29 36 > > The BAQ0 for the second C doesn't make sense to me, especially given > the tview output (previously posted).
Yes, it looks suspicious. I am not familiar enough with BAQ calculation to give a useful answer, though. Maybe Heng could comment? > Also, what does -x do? The manual says > -x, --ignore-overlaps disable read-pair overlap detection > Could you explain what this does and why it might affect BAQ computation? I believe it should not affect the calculation, only wanted to check that the 0 quality isn't coming from somewhere else. Petr > Andreas > > > On 16 October 2014 19:21, Petr Danecek <p...@sanger.ac.uk> wrote: > > Do you get the same output with -x? The base qualities are in set to 0, > > so that we do not count reads of the same molecule twice. > > > > petr > > > > > > On Mon, 2014-10-13 at 10:21 +0800, Andreas Wilm wrote: > >> Hi all, > >> > >> every now and then I see BAQ values of 0 in samtools' mpileups. I > >> thought I understood the overall concept, but now I'm not sure > >> anymore. Does a value of 0 indicate this base is misaligned for sure? > >> How can that ever be the case? Also, I see this happening in nicely > >> aligned regions (all MQ60; not a lot of SNVs) with no indels anywhere > >> nearby. It's seems to be mainly happening close to the end of reads > >> and I see the same behaviour in samtools 0.1.19 and 1.0. > >> > >> Here's an example: how can the second C every get a BAQ of 0? > >> > >> Pileup information first (with base qualities translated into phred > >> scores), followed by a screenshot of tview: > >> > >> # BAQ off > >> > >> samtools mpileup -B -Q 0 $BAM -f $REF -r chrX:46918110-46918110 > >> > >> chrX 46918110 G 21 cc,c,,,,,.c.,,..,..., 30 34 > >> 36 38 38 38 37 34 34 38 37 39 35 39 38 37 35 32 34 29 36 > >> > >> # BAQ on > >> > >> samtools mpileup -Q 0 $BAM -f $REF -r chrX:46918110-46918110 > >> chrX 46918110 G 21 cc,c,,,,,.c.,,..,..., 4 0 > >> 36 38 38 38 37 34 34 38 37 39 35 39 38 37 35 32 34 29 36 > >> > >> # extended BAQ > >> > >> samtools mpileup -E -Q 0 $BAM -f $REF -r chrX:46918110-46918110 > >> chrX 46918110 G 21 cc,c,,,,,.c.,,..,..., 4 0 > >> 36 38 38 38 37 34 34 38 37 39 35 39 38 37 35 32 34 29 36 > >> > >> > >> Screenshot of tview of the same region: > >> https://dl.dropboxusercontent.com/u/4119940/baq0.png > >> > >> Can anyone explain this? > >> > >> Many thanks, > >> > >> Andreas > >> > >> PS: This was cross-posted on https://www.biostars.org/p/115071/#115112 > >> > > > > > > > > > > -- > > The Wellcome Trust Sanger Institute is operated by Genome Research > > Limited, a charity registered in England with number 1021457 and a > > company registered in England with number 2742969, whose registered > > office is 215 Euston Road, London, NW1 2BE. > > > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
