Samtools Errors

[lwhitmore]

Hey I know there are alot of posts about samtool errors but I have yet to find a solution.

When I run
$ samtools view Reads.bam >reads.sam -bS
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!

Additionally when I tried the following two options I got errors as well-bash-$samtools view -T Reference.fa Reads.bam >reads.sam -bS
[sam_header_read2] 1 sequences loaded.
[sam_read1] reference 'SO:unsorted' is recognized as '*'.
Parse error at line 1: invalid CIGAR character
Aborted

$ samtools view -bt Reference.fa.fai Reads.bam > reads.sam
[sam_header_read2] 1 sequences loaded.
[sam_read1] reference 'SO:unsorted' is recognized as '*'.
Parse error at line 1: invalid CIGAR character
Aborted

Additionally I tried this but the sam file cam out blank
$ samtools view -h SRR519779test_Aligned_LW.dat.bam | awk -F'\t' 'BEGIN { dict[65] dict[147]} $2 in dict' >reads.sam

Thanks for any help
Leanne

[GenoMax]

It may be useful to add what program was used to generate your BAM files. Or were these downloaded from somewhere.

[lwhitmore]

Mosaik an IUPAC alignment program

[dpryan]

Does it directly produce BAM files or is there a SAM intermediate (I've never used Mosaik)? Also, which version of samtools are you using (if you just type "samtools" then it'll be near the top of the output)? For some reason samtools is seeing those as SAM files rather than BAM files, which should only happen if you supply "-S" on the command line.

[dpryan]

BTW, this:

samtools view Reads.bam >reads.sam -bS

doesn't make any sense as a command. I assume you actually meant:

samtools view -bS Reads.sam >reads.bam

which could produce the error messages you observed if "Reads.sam" is missing a header. If that's the case, just post the first dozen or so lines of Reads.sam

[swbarnes2]

Or, try

samtools view -bSh Reads.sam >reads.bam

Assuming you do have a header in your .sam file.