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
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
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?
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samtools
I'm sorry: samtools
I'm sorry: it's not.
You put it exactly how I wanted to put it, Pierre :)
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
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...
It's the other way around -
command sub-command
is how major tools operate. Seegit
,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 largeblastall
command.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.
Most linux distros come with package managers that take care of installing
samtools
with one command. Why avoid it?Hi mxs,
There is absolutely no need to remove a question after you received helpful reactions.
Cheers,
Wouter