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How Can I Convert Bam To Sam?

Any suggestions?

bam next-gen-sequencing sam
• 190,439 views • link
updated by Ram Ram • written by Biomed Biomed

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?

• 0 views • link
updated by Ram Ram • written by Manish • Manish

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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updated by Ram Ram • written by biobot 0.0.77.a.1099 biobot 0.0.77.a.1099

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

• 2 views • link
written by Fred Wang • Fred Wang

"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.

• 130 views • link
updated by Ram Ram • written by Aaronquinlan Aaronquinlan

4 answers

Use samtools from the command line:

samtools view -h -o out.sam in.bam
• 334 views • link
updated by Ram Ram • written by Brad Chapman Brad Chapman

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.

• 0 views • link
written by t.montserrat.ayuso • t.montserrat.ayuso

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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updated by Ram Ram • written by Atomic • Atomic

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.

• 0 views • link
written by Ram Ram

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
• 265 views • link
updated by Ram Ram • written by A. Domingues A. Domingues

Galaxy also does this.

• 61 views • link
updated by Ram Ram • written by Stephen Stephen

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

parallel --plus 'samtools view -h {} -o {...}.sam' ::: *.bam
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updated by Ram Ram • written by Tian • Tian

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