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. ------------------------------------------------------------------------------ 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
