Visualizing Variants

[jlelias]

I am working with IGV and have an alignment that I can visualize just fine. However, now I need a way to visualize just my variants in some kind of table or graph format. IGV is asking me for a .mut file, but I can't figure out what that is or how to get my data in that format. Please help me out.
Thank you!

[swbarnes2]

You probably want some program that will call SNPs from your .bam. GATK or samtools can do this. A .vcf (variant call format) file is the standard format.

[tarkvara]

If I may put in a plug for our own software, GATK integration is one of the new features of Savant 2. We tried to make it as easy as possible to run GATK on your BAM tracks and visualise the results within Savant.

[jlelias]

Thank you so much for your help! I am having issues with Samtools, though. I have the latest version, but it won't recognize the mpileup command (I have tried both with and without including "samtools" right before "mpileup"). The internet just suggests I download the latest version, but I'm positive I have it and I have tried re-downloading and re-compiling several times. Could you please help me out again?
Thank you!

[dpryan]

Could you show the exact command that you're using and the ensuing error message? That would be helpful in diagnosing your error.

[jlelias]

Sure!
$ samtools mpileup -f ADP1NCBI.fasta output.sorted.bam >JEoutput.mpileup
[main] unrecognized command 'mpileup'

Also, I've been trying variations of the command given directly on the Samtools website, i.e.:

samtools mpileup -uf ADP1NCBI.fasta output.bam | bcftools view - > var.raw.bcf bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf
[main] unrecognized command 'mpileup'
vcfutils.pl: command not found
bcftools: command not found

Thank you!

[swbarnes2]

What version of samtools do you have? Do you have the proper path to samtools in your command line?

[jlelias]

I have samtools-0.1.18
I'm not sure about the path . . .I have tried my commands both outside and inside the "samtools-0.1.18" folder that was created when I compiled the download using "tar -xvjf samtools-0.1.18.tar.bz2" command. However, when I look in this folder, there are no green names, so I don't know where my executables could be. I've tried "make", "install", "make install", and "configure" for my samtools file to make the executables appear, but nothing happens.
Thank you for your time. I am a beginner and am likely confusing something simple. . .

[jflowers]

Are you installing on a unix-based system? (had to ask). Which one?

[jlelias]

Yes, I am using unix . I downloaded it from Ubuntu. So, I'm not sure but I think its the 32-bit.

[swbarnes2]

I'm pretty sure that tar will only uncompress the folder, it won't install anything. You need to call 'make' in the samtools folder. It's possible you may have to tweak the makefile. I always get complaints about the curses file, a small change in the makefile fixes that for me. There's another thread around here somewhere about installing samtools.

[jflowers]

If youre using the latest Ubuntu version (11.10), I just tried quickly installing via the software center and it worked fine. Maybe not the most satisfactory but it should get you up and running.

[jlelias]

Thank you so much for your replies! I
1) downloaded the latest version of unix
2) changed the makefile according to directions given in a different seq forum
3) downloaded zlib and compiled/installed it (all the executables for the zlib appear in green.)
4) deleted my old samtools folders and downloaded them brand new.
5) used the command: tar -xvjf samtools-0.1.18.tar.bz2
6) Went into the samtools folder and used the command "make"

I received the following error and still no executable appear. I also tried using the "make" command with the zlib in the samtools folder.

make[1]: Entering directory `/home/lab/Desktop/linux files/samtools-0.1.18'
make[2]: Entering directory `/home/lab/Desktop/linux files/samtools-0.1.18'
gcc -c -g -Wall -O2 -l/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl-log -I. bgzf.c -o bgzf.o
<command-line>:0:5: warning: missing whitespace after the macro name [enabled by default]
In file included from bgzf.h:29:0,
from bgzf.c:36:
./zlib.h:34:19: fatal error: zconf.h: No such file or directory
compilation terminated.
make[2]: *** [bgzf.o] Error 1
make[2]: Leaving directory `/home/lab/Desktop/linux files/samtools-0.1.18'
make[1]: *** [lib-recur] Error 1
make[1]: Leaving directory `/home/lab/Desktop/linux files/samtools-0.1.18'
make: *** [all-recur] Error 1

I appreciate your help so much!!

[dpryan]

That error is telling you that the compiler can't find zconf.h in the normal search path. zconf.h is usually located in /usr/include or /usr/local/include, so check to make sure it's somewhere sensible on your system and that gcc knows to look there.

[jlelias]

I appreciate your suggestion! I moved zlib to both those locations.
However, now when I try to install samtools (I'm still trying to get the executables to show up) using the "make" command, I get the following errors: (to save space I took out just the errors)

make[2]: Nothing to be done for `lib'.
cd: 8: can't cd to /home/lab/Desktop/JL
cd: 8: can't cd to misc
make[1]: *** [lib-recur] Error 2
make: *** [all-recur] Error 1

I get these errors wether I am using the original makefle, or the altered one described in a different SEQ forum
Thanks again for your time!