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
