Re: [Samtools-help] FollowUp - Running samtools mpileup on BAM that contains colorspace

[Colin D. <col...@ho...>]

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: sam...@li...
> From: mi....@gm...
> 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/
> 
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