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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Resource bundle error download

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9 comments

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    Genevieve Brandt (she/her)

    Hi Linda Do, I am not able to reproduce this issue on my end so I cannot determine where the problem is coming from. The bucket you linked to is public and all files should be available.

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    Brian Wiley

    Hi Linda Do,

    I installed Google storage util following this https://cloud.google.com/storage/docs/gsutil_install and then you can get download to current directory with:

    gsutil cp gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.dbsnp138.vcf .

    and for hg38

    gsutil cp gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf .

    Genevieve-Brandt-she-her, any way we can have this Homo_sapiens_assembly19.dbsnp138.vcf file compressed with bgzip so its not 10 GB for download?  It takes long time to compress it.

     

     

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    Genevieve Brandt (she/her)

    Hi Brian Wiley,

    I can put in a request for this change and bring it up with my team. Our GATK Support Team is not the group that maintains these data resources, so I cannot guarantee any timeline for this. Here is our support policy for more details: https://gatk.broadinstitute.org/hc/en-us/articles/360038469272-What-types-of-questions-will-the-GATK-frontline-team-answer-

    Genevieve

     

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    Genevieve Brandt (she/her)

    Hi Brian Wiley, wanted to give you a quick update. After bringing this up with the team, I found that they agreed and would prefer a zipped version of the file. Thank you for bringing this issue to our attention! We are looking into changing it but still cannot guarantee a timeline.

    Genevieve

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    Linda Do

    Thank you Genevieve Brandt and Brian Wiley.

    You both were very helpful. I was able to successfully download the files.

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    Genevieve Brandt (she/her)

    Great! Thanks for the update Linda Do.

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    Genevieve Brandt (she/her)

    Brian Wiley we were able to update the Homo_sapiens_assembly38.dbsnp138.vcf with Homo_sapiens_assembly38.dbsnp138.vcf.gz, it's in the bucket now. 

    Thanks for bringing this to our attention, hopefully it helps the download speed!

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    Aravind Sundar

    Hi, I was wondering if instead of the "Homo_sapiens_assembly38.dbsnp138.vcf.gz" file we can use the "00-All.vcf.gz" file in this location(https://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/) from the dbSNP database? 

    For context, I am working with whole exome sequencing data and am curious if I can use the updated version of the common SNP's from the database if at all I can use the above one since I am working with Whole Exome Sequencing data and not Whole Genome Sequencing data for the Baserecalibration step of the variant calling pipeline?

    Any and all help will be appreciated. Thank you

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    Kevin Lydon

    Hi Aravind Sundar,

    It might work, but I can't say with full certainty.  The baserecalibration could benefit from the more up-to-date SNPs, but there is the possibility that something has changed between those that could maybe cause issues.  The most likely issue could be contig names, so I would recommend checking the contig names between those files before running to see if there are differences.

    Hope this helps!

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