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). 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? 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. -- Andreas Wilm andreas.w...@gmail.com | m...@andreas-wilm.com | 0x7C68FBCC ------------------------------------------------------------------------------ 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
