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Question: Using Samtools to convert bam to sam file
1
gravatar for gerritvanderende
4.4 years ago by
gerritvanderende • 10
United States
gerritvanderende • 10 wrote:

I am trying to convert a bam file to sam file in samtools and I need to designate the directory where the sam file is saved to. How would this be accomplished in samtools?
next-gen • 10k views
ADD COMMENT • link •
modified 4.3 years ago • written 4.4 years ago by gerritvanderende • 10

what did you try so far ?....

ADD REPLY • link written 4.3 years ago by Pierre Lindenbaum ♦ 124k

i just tried view and the bam file name, view and the bam file directory location. I'm new to all of this so I apologize if I am asking annoying or obvious questions.

ADD REPLY • link modified 4.3 years ago • written 4.3 years ago by gerritvanderende • 10
3
gravatar for skbrimer
4.3 years ago by
skbrimer • 610
United States
skbrimer • 610 wrote:

Hi, 

To include the header you can use this

samtools view -h -o yourDir/test.sam test.bam
ADD COMMENT • link written 4.3 years ago by skbrimer • 610
1
gravatar for Aurélien Guy-Duché
4.3 years ago by
Aurélien Guy-Duché • 30
France
Aurélien Guy-Duché • 30 wrote:

Hello,

samtools view test.bam > yourDir/test.sam
ADD COMMENT • link written 4.3 years ago by Aurélien Guy-Duché • 30
2

what about the BAM header. Aurelien, now, go back writing your internship report :-)

ADD REPLY • link written 4.3 years ago by Pierre Lindenbaum ♦ 124k
1

Now, this is cyberbullying !! :-)

ADD REPLY • link written 4.3 years ago by Ashutosh Pandey ♦ 11k
1

Sir, yes Sir ! :-)

ADD REPLY • link written 4.3 years ago by Aurélien Guy-Duché • 30
0
gravatar for gerritvanderende
4.3 years ago by
gerritvanderende • 10
United States
gerritvanderende • 10 wrote:

Thank you all for your help. I am learning programming languages so hopefully I won't have to ask continual questions.
ADD COMMENT • link written 4.3 years ago by gerritvanderende • 10
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