How Can I Convert Bam To Sam?

Question

[Biomed]

Any suggestions?

[Fred Wang]

when converting from sam to bam the default method compresses the resulting bam file. Compression could result in data loss.

[Aaronquinlan]

"Compression could result in data loss." This is only correct if a lossy compression algorithm is used. BAM natively employs zlib (~LZ77) compression, which is a _lossless_ compression algorithm. Thus, no data is lost.

[Manish]

Hi,

When I am converting Sam to Bam and back to Sam.I am loosing quality score of the Sam file. i.e. Input sam and the reversed sam does not match. Is this expected?

[biobot 0.0.77.a.1099]

Hi manish. You should open a new question for this. When you put your question in as an answer, people are unlikely to respond.

Answer 1

[Brad Chapman]

Use samtools from the command line:

samtools view -h -o out.sam in.bam

[elhameataie]

it does not work for me! why?!

[elhameataie]

oh I understand guys. before this command, we should install samtools in the bash. http://www.htslib.org/download/

[t.montserrat.ayuso]

You can use this:

To convert BAM to SAM you can use:

$ samtools view -h file.bam > file.sam 

You should include -h option to include the header in the SAM output.

And to convert SAM to BAM:

$ samtools view -b file_copy.sam > file_copy.bam

-b is the option to output BAM.

[Atomic]

Where is the command line? I'm sorry I don't know what I am doing and I just downloaded samtools but I cannot figure out where to input the $ samtools view -h file.bam > file.sam code, as I need to turn a file that is bam to a sam file for my mother.

[Ram]

Have you tried Googling "where is the command line"? Also, the fact that you need to convert a file for your mother is irrelevant here, so why mention it?

When you do find the command line, ensure you don't enter the $ at the beginning; that's just the symbol for the command line prompt and is not meant to be part of the command.

Answer 2

[A. Domingues]

If you want to do it in batch:

# convert BAM to SAM
for file in ./*.bam
do
    echo $file 
    samtools view -h $file > ${file/.bam/.sam}
done

Answer 3

[Stephen]

Galaxy also does this.

Answer 4

[Tian]

With parallel, remember to cite the paper, it's remarkable work.

parallel --plus 'samtools view -h {} -o {...}.sam' ::: *.bam