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Re: [Samtools-help] [Bio-bwa-help] making sense of CIGAR and MD tags from BWA alignment.
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From: Joseph F. <jos...@gm...> - 2013-03-13 17:55:54
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You lost me, Carlos. Am I missing something about the CIGAR codes? Please enlighten me if so ... ~Joe On Wed, Mar 13, 2013 at 10:48 AM, Carlos Pérez Cantalapiedra < cpc...@gm...> wrote: > I am still looking for someone who doesn't consider silly the lack of a > explicit code for mismatches in CIGAR spec. Would make things much easier... > > > 2013/3/13 Joseph Fass <jos...@gm...> > >> Hi Abhishek, >> >> Maybe I'm confused about your question, but both of the tags in your >> example are consistent with each other. If you include the reference >> sequence, then the CIGAR string completely specifies the alignment, because >> the second base will be an A in the read, and *not* an A in the >> reference. So it's just a matter of the CIGAR format specifying both >> (M)atches and (M)ismatches with the M character (which seems pretty silly >> to me, but maybe there was a good reason). There *must *be code / >> libraries out there that can do what you want (maybe Bioconductor's >> rsamtools??, or pysam, or some bioperl module?), but I'm not the best >> person to comment on that. >> >> Hope this helps, >> ~Joe >> >> >> >> On Tue, Mar 12, 2013 at 8:46 AM, Abhishek Pratap <ap...@lb...> wrote: >> >>> Hi Guys >>> >>> I am somewhat confused when I look at the CIGAR and MD string from a BWA >>> alignment. It is rather surprising that I dint had to compare these tags >>> before. >>> >>> For example I saw CIAGR : 150M as MD:1A148 and many other examples >>> which indicate one needs to parse both the tags in full to fully infer the >>> indels/mismatches in an actual alignment. Not sure why there are two >>> separate formats and why each one only captures part of the information. >>> >>> Just wondering if this is the way to go for inferring indels and >>> mismatches or I am missing something. Also if there any code out there >>> which can take the bam/sam file and spit out the percent mismatches / read >>> base location and similarly for indels, I would happily use it. >>> >>> PS: I did post a similar question on biostars last week but may be it >>> was not that exciting for folks there. Here is the link if you want to >>> comment there. http://www.biostars.org/p/65957/#65959 >>> >>> Thanks! >>> -Abhi >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester >>> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the >>> endpoint security space. For insight on selecting the right partner to >>> tackle endpoint security challenges, access the full report. >>> http://p.sf.net/sfu/symantec-dev2dev >>> _______________________________________________ >>> Bio-bwa-help mailing list >>> Bio...@li... >>> https://lists.sourceforge.net/lists/listinfo/bio-bwa-help >>> >>> >> >> >> -- >> Joseph Fass >> Lead Data Analyst >> UC Davis Genome Center - Bioinformatics Core >> http://bioinformatics.ucdavis.edu/ >> jn...@uc... >> phone ~ 530.752.2698 >> >> >> ------------------------------------------------------------------------------ >> Everyone hates slow websites. So do we. >> Make your web apps faster with AppDynamics >> Download AppDynamics Lite for free today: >> http://p.sf.net/sfu/appdyn_d2d_mar >> >> _______________________________________________ >> Bio-bwa-help mailing list >> Bio...@li... >> https://lists.sourceforge.net/lists/listinfo/bio-bwa-help >> >> > -- Joseph Fass Lead Data Analyst UC Davis Genome Center - Bioinformatics Core http://bioinformatics.ucdavis.edu/ jn...@uc... phone ~ 530.752.2698 |