[Risha]

I also came across the 'missing header' error. I found that that when converting BAM-> SAM, I had forgotten about printing the headers. This fixed it for me:


BAM -> SAM:

Note : -h print header for the SAM output

samtools view -h in.bam > out.sam

SAM -> BAM (even SAM produced from BWA):

samtools view -bS in.sam > out.bam

[Lovro]

i have the same problem...

this is from the man samtools:
o Import SAM to BAM when @SQ lines are present in the header:

samtools view -bS aln.sam > aln.bam

If @SQ lines are absent:

samtools faidx ref.fa
samtools view -bt ref.fa.fai aln.sam > aln.bam

where ref.fa.fai is generated automatically by the faidx command.

However, i don't know which ref.fa to use.
The sam i'm trying to convert to bam, sort and index was generated by a foreign seq searching program, readscan, which uses host and pathogen ref seqs and try to map to both of them.

the actual sam file i'm trying to convert is "ambiguous.sam" which contains reads mapped to both ref seqs.

can somebody please explain what is going on... what are @SQ lines, why does samtools need them to convert to bam and index the file, why am i expected to provide a ref.fa ....

its really confusing

tnx !

[mastal]

If you are aligning to something like the human genome, then you would usually have one @SQ line for each chromosome in the sam file header.

If you have the sequences of the host and pathogen the reads were mapped to, you could combine them into a ref.fa file, and run samtools faidx.