Converting Sam To Bam

Question

[Haluk]

Hi,

I have set of sam files and I would like to convert them into bam files with the following script. But it didn't create bam files? What I have made wrong?

for file in `ls ~/wgs/sam`; 
do 
   ~/bin/samtools-0.1.18/samtools view -bS ~/wgs/sam/$file \
   > ~/wgs/bam/$FILE.bam; 
done

Thanks

[Aaronquinlan]

Çould you comment on whether any files are created at all? If yes, what type of files are they?

[Haluk]

Actually, I had a typo in my script. Here is the right one. Sorry about that.

for file in `ls ~/wgs/sam`
do
  ~/bin/samtools-0.1.18/samtools view -bS ~/wgs/sam/$file > ~/wgs/bam/$file.bam
done

[Aaronquinlan]

You use $file to define the SAM file, yet $FILE for the BAM. s/$FILE/$file/ and you should be good.

[Haluk]

As a result, I had bam files for each sam files.

[Andreas]

And that's what you wanted, right

[Haluk]

yes, Andreas, problem solved.

Answer 1

[Pascal]

Haluk, you should use the option -o FILE output file name [stdout] instead of redirecting the stdout to the bam file.

[brentp]

that doesn't affect whether it's BAM output or not.

[conchoecia]

I think this was in reference to the possibility of stderr also directing to the output file when ">" instead of "-o" is used. Found something about it here: https://sourceforge.net/p/bio-bwa/mailman/message/32092344/

Not sure if it's still a problem though!

Answer 2

[Jautis]

Not sure what you did wrong, but I use samtools view -bT reference.fa test.sam > test.bam and it works pretty well