strange bwa/samtools behaviour (?)

[francesconea]

Hello everyone
First of all, I'd like to thank you for this super-useful community everyone's contributing to build up. It's a kind of next-gen sequencing for me
Now, coming to my question:
I'm quite new in next-gen sequencing and I'm working with Illumina data (paired-end, 76bp long reads, whole exome) and I cannot have any of my aligned bam/sam files with header included. That is, I have all the pretty @SQ lines and @PG line at the end of the header. What I can't gain is the @HD/tVN/SO line at the very beginning of the header.

In addiction, if i try to do
bwa aln - bwa sampe - samtools view - samtools sort in a separate way, when I try to give a look to my new-beautiful-bam-file's header I'll receive always this message:

samtools view -H prova.bam <- my command
[bam_header_read] EOF marker is absent.

while, when I sort it, I get this other one:
samtools sort prova.bam prova_sorted <- my command

[bam_header_read] EOF marker is absent. The input is probably truncated.

All of this doesn't happen at all if I do that in a piped way...even if the @HD/tVN:/tSO line is still missing

Any ideas would be particularly appreciated