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sam to bam

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

alignment ngs
• 2,367 views • link
updated by h.mon h.mon • written by mxs mxs

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.

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written by Pierre Lindenbaum Pierre Lindenbaum

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

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written by Kevin Blighe Kevin Blighe

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

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written by mxs mxs

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.

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written by Ram Ram

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.

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written by Kevin Blighe Kevin Blighe

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...

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written by Pierre Lindenbaum Pierre Lindenbaum

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

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written by Ram Ram

Hi mxs,

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

Cheers,
Wouter

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written by WouterDeCoster WouterDeCoster

1 answer

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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written by h.mon h.mon

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

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written by mxs mxs

No one really said SRA.

something else unrelated to bioinformatis [sic]

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

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written by Ram Ram

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