Is that possible to run analyses on 1000 Genomes dataset using Firecloud?

Hi, Firecloud Team. I've been used Firecloud to analyse TCGA dataset. I'm wondering if it's possible to run the 1000 Genomes dataset using Firecloud?

Such as gs://genomics-public-data/1000-genomes/bam/NA07000.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.bam.

Thank you.

Best Answer

Answers

  • jemimalwhjemimalwh ChinaMember

    @Geraldine_VdAuwera said:
    Sure, you can analyze any dataset you want. Although FireCloud is mainly described as a cancer analysis platform, there is no technical limitation preventing you from analyzing germline data. We are in fact working on adding some resource workspaces for analysis with GATK.

    So happy to hear that. Thank you so much. Could you provide some examples? I've tested to upload my sample.txt file containing 1000 genomes dataset information, but it showed Error message:

    #

    Error: Could not resolve some entity references
    Hide Details
    Code: 400
    Occurred: 2017年4月27日 GMT+8 下午2:31
    Source: rawls
    Cause:
    Message: participant NA07000 not found
    Source: rawls

    #

    This is the input file:

    entity:sample_id participant_id WXS_bam_path
    NA07000 NA07000 gs://genomics-public-data/1000-genomes/bam/NA07000.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.bam

    Thank you.

  • Geraldine_VdAuweraGeraldine_VdAuwera admin Cambridge, MAMember, Administrator, Broadie admin
    Ah, this means you need to upload the list of participants first. In future we'll get participant IDs to auto populate, but for now you have to enter it explicitly.
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