[Victory]

Thank you. I will try that.

[nilshomer]

I use the import command to make BAM file.
samtools import <in.ref_list> <in.sam> <out.bam>
Do I have to use specific command to install the SAM program or just put the program folder on the directory?

You have to copy the binary to an directory where *other* binaries are installed (like /usr/local/bin). You have to make sure that your PATH environment variable includes the above path. Then you can just "samtools" instead of the "/home/<ETC>/samtools"

[Victory]

I use the import command to make BAM file.
samtools import <in.ref_list> <in.sam> <out.bam>
Do I have to use specific command to install the SAM program or just put the program folder on the directory?

[nilshomer]

Thank you. I use SUN cluster computer. I have already copy whole folder of SAM version 0.1.6 to my working directory. However, it still doesn't work. I'm not sure which one is the install directory.

Please be more verbose. What commands are you executing to install samtools after copying the SAM folder. You may have to get your cluster administrator to install samtools cluster-wide. I typically have a local install directory that is included in my PATH environmental variable.

[Victory]

Thank you. I use SUN cluster computer. I have already copy whole folder of SAM version 0.1.6 to my working directory. However, it still doesn't work. I'm not sure which one is the install directory.

[nilshomer]

Are there anyone know how to install SAM tool? I read in the SAM document and it didn't say anything about that. Thank you.

Download it from http://samtools.sourceforge.net/. Copy the binaries to your typical install directory (which depends on your system).

[Victory]

Install SAM tool

Are there anyone know how to install SAM tool? I read in the SAM document and it didn't say anything about that. Thank you.

[totalnew]

I tried to use sort command :
samtools sort aln.sam aln.sam.sorted
i also got
Segmentation fault
is there anybody had this probelm before?

You should sort bam file, try this

samtools sort -n aln.bam sorted

then mv the sorted.bam file to whatever name you want.

[xuer]

I tried to use sort command :
samtools sort aln.sam aln.sam.sorted
i also got
Segmentation fault
is there anybody had this probelm before?

[kraigrs]

When I attempt to align mated paired-end sequence reads and output the file
in SAM format, I receive a segmentation fault. If I try the same thing
without the -S/--sam option, it works fine. Here is what I am getting:

EEB-WITT5:Bowtie wittkopp-lab$ ./bowtie -q -k 1 --sam --best
--solexa1.3-quals dmel-all-CDS-r5.21 -1
./mel_sim_data/Hybrids/s_2_1_sequence.txt -2
./mel_sim_data/Hybrids/s_2_2_sequence.txt > s_2_sequence.sam

Segmentation fault

Any help in this matter would be greatly appreciated! Again, I would like
this output to be in SAM format. I tried converting the bowtie output to
SAM but the bowtie2sam.pl script from SAMtools doesn't do that for me.

[totalnew]

hi there again...


Step 3:
../../samtools-0.1.5c_x86_64-linux/samtools view -S -h Risk_no_haplos.sam \
is giving
missing header? Abort!

../../samtools-0.1.5c_x86_64-linux/samtools pileup -S -cf Final Risk_no_haplos.sam
is giving
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!


aargh

EDIT: Woohoo, finally figured it out... Apparently i had to use faidx before i could use pileup straight away... The question remains if using BWA is a wise thing for the presented problem...

Apparently, you shouldn't use samtools view sam file, that is for bam file. To pileup, you would either make bam file or get indexed reference sequence (.fai).

[totalnew]

I have a quick question. How can I use 'samtools view' for converting bam file to sam file? I tried some times but I failed to do it...

That is way simple, try this linux command

samtools view test.bam > test.sam

[joa_ds]

hi there again...

The reasons I am trying BWA (still hasn't worked... ) is because I am analyzing illumina data for counting variant frequencies for a pool of several patients.

So far so good, BowTie gives 15%, Maq gives 40% and Sanger validation gives 0% for a certain variant. We have around 1000 variants, so this is kinda annoying.

I am doing a very simple thing: I align the reads using BowTie and i just parse the output file and count the variant frequencies. Some other people used MAQ and in the lab they verified using Sanger.

Before I spend another 10h trying to figure out why this BWA thing ain't working, is it worth trying to determine variant frequencies in a pool? And if so, what is the best strategy to do so.

And on the BWA/samtools thingie. I tryed using the -S flag but i keep getting "Segmentation fault"

I must be doing something totally wrong here...


Step 0:
/data/illumina/bwa-0.4.9/bwa index -a is Final

Step 1:
/data/illumina/bwa-0.4.9/bwa aln -t 12 Final Risk_no_haplos.txt > Risk_no_haplos.sai

Step 2:
/data/illumina/bwa-0.4.9/bwa samse Final Risk_no_haplos.sai Risk_no_haplos.txt > Risk_no_haplos.sam

Step 3:
../../samtools-0.1.5c_x86_64-linux/samtools view -S -h Risk_no_haplos.sam \
is giving
missing header? Abort!

../../samtools-0.1.5c_x86_64-linux/samtools pileup -S -cf Final Risk_no_haplos.sam
is giving
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!


aargh

EDIT: Woohoo, finally figured it out... Apparently i had to use faidx before i could use pileup straight away... The question remains if using BWA is a wise thing for the presented problem...

[nilshomer]

I have a quick question. How can I use 'samtools view' for converting bam file to sam file? I tried some times but I failed to do it...

You can, but include the header ("-h").

[yasu]

I have a quick question. How can I use 'samtools view' for converting bam file to sam file? I tried some times but I failed to do it...