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Use samtools to access bam file in aws s3 storage

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?

I followed the instruction in 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.

Best,
Xing

samtools
• 7,148 views • link
updated by Ram Ram • written by xing • xing

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.

• 0 views • link
written by igor igor

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

• 0 views • link
written by lh3 lh3

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?

• 1 views • link
written by cmdcolin cmdcolin

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