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A question about the database bed file:cn2_mask_g1k_v37.mask.bed

ahdaahda ChinaMember

I just want to confirm that if the file cn2_mask_g1k_v37.mask.bed( which come from the link [ftp://ftp.broadinstitute.org/pub/svtoolkit/cn2masks/cn2_mask_g1k_v37.mask.bed] can serve as segmental_duplication_file specified by parameter "--segmental-duplication-track" of the tools AnnotateIntervals?
Asking because I use this as the segmental duplication files, then I found that, some filtered intervals are not repeat regions,like this two filtered intervals:
chr12 25378298 25378957 0.313636 1.000000 0.734848
chr12 25397958 25398579 0.337621 1.000000 1.000000

Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @ahda

    We are looking into this and will get back shortly.

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @ahda

    The seg dup file that we are use can be found here:
    gs://gatk-best-practices/germline-copy-number/hg19.nochr.SegDups.elements.no_gl.bed
    gs://gatk-best-practices/germline-copy-number/hg19.nochr.SegDups.elements.no_gl.bed.idx

  • ahdaahda ChinaMember

    I‘m so sorry but how can I get the link?
    I tried to visit it directly while I failed, then I searched it in google,but it seems i cannot find it correctly.
    I met the gs://XXXX a lot of times here,but i never know how to visit them.

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @ahda

    That is a public google bucket. Here take a look at this doc for information on how to access data from a google bucket: https://cloud.google.com/storage/docs/gsutil/commands/cp

  • ahdaahda ChinaMember

    I am so sorry I cannot visit this google bucket. Maybe due to my network, I have tried a lot of ways to connect but I failed.
    So can I have other ways to get this file? Thanks so much for your patiently and kindly help!

    Cannot reach https://www.google.com (ServerNotFoundError)
    Cannot reach https://accounts.google.com (ServerNotFoundError)
    Cannot reach https://cloudresourcemanager.googleapis.com/v1beta1/projects (ServerNotFoundError)
    Cannot reach https://www.googleapis.com/auth/cloud-platform (ServerNotFoundError)
    Cannot reach https://dl.google.com/dl/cloudsdk/channels/rapid/components-2.json (ServerNotFoundError)
    
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