SAMtools missing bcftools

[khadeeja]

Hi everyone,
I've installed samtools, but it is not identifying the bcftools command. Would be great if anyone of you could point out a solution to my problem.
And btw, I'm new to this forum, and am not very familiar with it yet, so my apologies if I'm posting this message where I'm not supposed to.
Thanks in advance
K.

[nilshomer]

Hi everyone,
I've installed samtools, but it is not identifying the bcftools command. Would be great if anyone of you could point out a solution to my problem.
And btw, I'm new to this forum, and am not very familiar with it yet, so my apologies if I'm posting this message where I'm not supposed to.
Thanks in advance
K.

Welcome, what is the error you see in you terminal? Also, it is probably good to create a new thread in this case since it looks like the previous thread in which you post was too unrelated (i.e. you hijacked the thread).

[khadeeja]

Hi,
Sorry and thanks.
It just says that "bfctools:command not found." I had the problem earlier with mpileup but installing some libraries and recompiling samtools solved that problem. As for this, I have no clue. I have the latest version of samtools (0.1.16). Could it be because of a missing library?
Once again, thanks for the reply.
K.

[nilshomer]

Check the "bcftools" sub-directory in the samtools installation directory.

[khadeeja]

The directory is there: /samtools/bcftools.
I installed libbza-dv, zlib1g-dv and libncursn5-dv earlier and recompiled samtools to get mpileup working. No idea what these libraries are bcoz I'm new to linux as well. Just followed some instructions given on a website.

[nilshomer]

Try "/samtools/bcftools/bcftools" and it should work if compiled correctly.

[khadeeja]

Oh, yes, it does. Thanks, nilshomer

[ninjapanda57]

Help

Also sometimes when It gives me that error it's because i haven't properly typed the command it should look like this :

samtools mpileup -u -f <reference_file>.fa <bam_file>.bam | bcftools -cvg | less if you want to just look at it on your page. the -cvg makes it in a really nice format. the -u and -f make sure you can have an output file.

[sadiexiaoyu]

Try "/samtools/bcftools/bcftools" and it should work if compiled correctly.

Hi, nishomer,

I also met the same problem that the bcftools command not found. I tried to change pathway, but still did not work. And there is bcftools sub-file in the samtools file, but no bcftools file in the sub-file. Is there bcftools file in the bcftools subfile?

Thanks!

Best,

Sadiexiaoyu