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How to index a CRAM file on Terra with samtools?

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7 comments

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    Jason Cerrato

    Hi Aisling,

    We'll take a look at this and get back to you with any questions or suggestions as soon as we can.

    Kind regards,

    Jason

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    Jason Cerrato

    Hi Aisling,

    Which notebook runtime are you using? Are you using the default image? 

    Kind regards,

    Jason

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    Aisling O'Farrell

    Yes, it's the default image.

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    Jason Cerrato

    Hi Aisling,

    Just wanted to drop in and let you know we're taking a closer look at the default images to make sure they'll work for your purposes. I'm also planning to take a look to see if there are any readily-available WDLs that can alternatively be used for your indexing. Are you currently blocked until either one of these options are presented? I will also converse with the developers to see if going the custom docker container route would work.

    Kind regards,

    Jason

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    Aisling O'Farrell

    I am in contact with Walt from UCSC, meaning I can edit the WDL from my end. I have done so and I'm currently in the process of testing it.

    So I'm not blocked at the moment, as I've found an alternative route.

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    Jason Cerrato

    Hi Aisling,

    Glad to hear. Would you still like for me to reach out regarding the default images once we've confirmed they would work for this purpose?

    Kind regards,

    Jason

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    Aisling O'Farrell

    Yes, that'd be brilliant. Always good to have more information. Thanks!

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