Use samtools to access bam file in aws s3 storage
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5.2 years ago
xing ▴ 10

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.

Any

Best,

Xing

samtools • 3.7k views
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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.

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

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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?

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