sam to bam

Question

[mxs]

Hi,

Anyone knows a simple standalone sam2bam conversion tool. I do not want to download and install the whole samtools just to do a simple conversion (under the assumption that it is simple)

thnx

[Pierre Lindenbaum]

simple standalone sam2bam conversion tool

samtools

. I do not want to download and install the whole samtools just to do a simple conversion

I'm sorry: samtools

(under the assumption that it is simple)

I'm sorry: it's not.

[Kevin Blighe]

You put it exactly how I wanted to put it, Pierre :)

[mxs]

yea but even the blast developers realized at one point that it is just too impractical and old school to put everything into one box like blastall was before. so i figured maybe there was some movement toward 21 century with samtools too :) but thnx

[Pierre Lindenbaum]

to put everything into one box like blastall was before.

samtools is based on C library : htslib which contains everything to convert sam->bam.

the time you'll need to re-invent samtools will be longer than installing samtools.

the time you needed to write this question on biostars could be greater than the time needed to install samtools...

[Ram]

It's the other way around - command sub-command is how major tools operate. See git, brew, apt-get, etc BLAST seems to be a special case where the algorithm changes so much between sub-commands that it doesn't make sense to have just one large blastall command.

[Kevin Blighe]

SAMtools is one of the most successful and fundamental [to have, in bioinformatics] programs of all time and is constantly being updated. SAMtools / BCFtools is even a superior variant caller when compared to other tools, in my experience.

[Ram]

Most linux distros come with package managers that take care of installing samtools with one command. Why avoid it?

[WouterDeCoster]

Hi mxs,

There is absolutely no need to remove a question after you received helpful reactions.

Cheers,
Wouter

Answer 1

[h.mon]

SAMtools is standalone, is simple, well-documented and is found on several package managers. I really wonder what could be simpler than that. A web server?

[mxs]

i don't need it for SRA. i need it for something else unrelated to bioinformatis and it fits perfectly but i do not need anything else except sam2bam utility :) I mean this is like seqan u need one ting but have to drag the entire library with it.... thnx anyway

[Ram]

No one really said SRA.

something else unrelated to bioinformatis [sic]

Off topic on the forum then, let's close the question?