Question: Use samtools to access bam file in aws s3 storage
gravatar for xing
2.4 years ago by
xing0 wrote:

I have a private aws bucket with aws_access_key_id, aws_secret_access_key, and region

How set I set up samtools 1.3 to make it work on bam files on aws s3 storage?

follow the instruction in A: Tool for random access to indexed BAM files in S3?

I can make the following command work $ samtools view s3://1000genomes/phase1/data/NA12878/exome_alignment/NA12878.mapped.illumina.mosaik.CEU.exome.20110411.bam 20:1000-100000 # works

but I can not make samtools work on my private bucket.




samtools • 1.4k views
ADD COMMENTlink written 2.4 years ago by xing0

According to the post you linked to, it should only work for public buckets. Thus, it makes sense that it doesn't work for your private bucket.

ADD REPLYlink written 2.4 years ago by igor7.3k

You need to create a credential file in your home directory. I forgot the file name. Ask samtools-help.

ADD REPLYlink written 2.4 years ago by lh331k

I am curious, the command you have pasted does not work for me in samtools 1.9 or on any other files which I know are valid links. Any idea why?

ADD REPLYlink written 20 days ago by cmdcolin1.1k
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