How Can I Convert Bam To Sam?
4
33
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13.9 years ago
Biomed 5.0k

Any suggestions?

bam next-gen-sequencing sam • 175k views
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1
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when converting from sam to bam the default method compresses the resulting bam file. Compression could result in data loss.

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11
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"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.

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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?

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10
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Hi manish. You should open a new question for this. When you put your question in as an answer, people are unlikely to respond.

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62
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13.9 years ago

Use samtools from the command line:

samtools view -h -o out.sam in.bam
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it does not work for me! why?!

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3
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oh I understand guys. before this command, we should install samtools in the bash. http://www.htslib.org/download/

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0
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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.

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0
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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.

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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.

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10
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11.6 years ago
A. Domingues ★ 2.7k

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
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3
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12.8 years ago
Stephen 2.8k

Galaxy also does this.

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2.8 years ago
Tian ▴ 50

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

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