Hi, back in the day I used SOLiD data quite a bit with samtools and had no trouble calling variants.
Possible solutions: - try samtools calmd to recalculate MD tags in the BAM - perhaps try an older samtools version, e.g. 0.1.19 (?) - use another aligner - we used novoalignCS which worked like a charm - commercial, but with free trial - What is the exact error msg ? Colin > To: samtools-help@lists.sourceforge.net > From: mi.gruenstae...@gmail.com > Date: Mon, 22 Aug 2016 21:46:18 +0200 > Subject: [Samtools-help] FollowUp - Running samtools mpileup on BAM that > contains colorspace > > Hi all, > I am following up on my question regarding the ability of 'samtools' to > view or call the consensus of aligned reads in BAM format when the BAM > file contains the reads also in colorspace. > > As noted in my question, 'samtools mpileup' appears unable to map these > reads against the very reference genome that the reads were aligned to. > Could this be the result of the BAM file containing colorspace info or > do I have to consider alternative reasons? > > Below please find an excerpt of the corresponding SAM file: > > user$ samtools view -h -o aln.sam aln.sorted.bam > user$ head aln.sam > @HD VN:1.0 SO:coordinate > @SQ SN:my_ref LN:152765 M5:d7d7fd29f9460f1026bf65295053b8d9 > @RG ID:ZVHAC3A4NMS SM:unknown PL:solid > @PG ID:MosaikAligner VN:2.2.26 > CL:/home/user/git/MOSAIK/bin/MosaikAligner -in my_data.dat -out aln -ia > my_ref.dat.cs -ibs my_ref.dat > 718_406_864 113 my_ref 380 8 1S38M1S = 548201 > NAAAAAAGGAGCAATAGCTTCCCTCTTGTTTTATCAAGAN > !>>99;==<667783322<88==4++55:))>>A;;>AB! RG:Z:ZVHAC3A4NMS NM:i:0 > MD:Z:38 ZA:Z:<@;8;;;1;;><&;7;;;1;34M1S;34> > CS:Z:T0220123300011022200202323301322020000032 > CQ:Z:!@BA>;AA>?):;5>+4B=>8<?233=8776<A=>;9?>=3 > 800_1371_875 113 my_ref 380 8 1S38M1S = 520173 > NAAAAAAGGAGCAATAGCTTCCCTCTTGTTTTATCAAGAN > !==7114455226:**22;::==337:88!!==>999@@! RG:Z:ZVHAC3A4NMS NM:i:0 > MD:Z:38 ZA:Z:<@;8;;;1;;><&;7;;;1;34M1S;34> > CS:Z:T0220123300011022200202323301322020000032 > CQ:Z:!?@@99>@==!98:;73?=>:;<22*<:62:5?4>17A==; > > > Thanks in advance, > > Michael Gruenstaeudl > http://blogs.fu-berlin.de/gruenstaeudl/ > > > On 2016-08-21 20:14, Michael Gruenstaeudl wrote: > > Hi all, > > I have some SOLiD data from way back and aligned the reads in colorspace > > to a reference genome via 'MosaikAligner'. The output of said assembler > > is a 'BAM' file that, if sorted, indexed (both via 'samtools') and > > eventually converted to 'SAM', exhibits information in colorspace. > > > > Now, I would like to call the consensus of the aligned reads via > > 'samtools mpileup', but find that 'samtools' cannot map any of the reads. > > > > I presume that this error is the result of colorspace information > > contained within the 'BAM' file and that 'mpileup' is unsuccessful due > > to this circumstance. How would you proceed here? > > > > *NOTE 1:* Said 'BAM' file can be open and viewed without problem via > > 'BamView', which I presume indicates the integrity of the 'BAM' file. > > > > Thanks in advance, > > > > Michael Gruenstaeudl > > http://blogs.fu-berlin.de/gruenstaeudl/ > > ------------------------------------------------------------------------------ > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help
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