Question: Running samtools mpileup on BAM that contains colorspace
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gravatar for Michael Gruenstaeudl
7 months ago by
Berlin, Germany
Michael Gruenstaeudl10 wrote:

I have some SOLiD data from way back and aligned the reads in colorspace to reference genome my_ref 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.

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==;

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.

user$ samtools mpileup -uf my_ref aln.sorted.bam
BCF##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed",IDX=0>
##samtoolsVersion=1.3.1+htslib-1.3.1
# multiple_lines_here_starting_with_##INFO=   
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  unknown
<mpileup> Set max per-file depth to 8000
user$

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.

EDIT 1: To clarify my post: I am primarily interested in the question if the inability of 'samtools mpileup' to map the reads against the very reference genome that the reads were aligned to could be the result of the BAM file containing colorspace info, or do I have to consider alternative reasons?

ADD COMMENTlink modified 7 months ago • written 7 months ago by Michael Gruenstaeudl10
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