Does the Broad still recommend aligning WXS/WES data to b37/hg19?

pwaltmanpwaltman New York, NYMember

According to the article on the the resource bundle (https://software.broadinstitute.org/gatk/download/bundle), you still recommend aligning to b37/hg19 for WXS/WES data (with either hg38 or b37/hg19 for WGS data). However it appears that that recommendation is over 2 years old (the page states that that recommendation is from August 2016).

Do you still recommend using b37/hg19 for WXS/WES data? I'm asking because it appears that a number of the articles on the site assume that one is working with bams that have been aligned to hg38, e.g. this tutorial on using mutect2: https://software.broadinstitute.org/gatk/documentation/article?id=11136

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  • AdelaideRAdelaideR Unconfirmed, Member, Broadie, Moderator admin

    @pwaltman Thank you for your question. I have reached out to the resource bundle team to see if the website recommendation is up to date for WXS/WES data.

  • AdelaideRAdelaideR Unconfirmed, Member, Broadie, Moderator admin

    @pwaltman They responded that they are looking into it.

  • manbamanba Member
    in fact,I also tried to change the header length of bam file to the same with reference, but I do not know why it also said

    A USER ERROR has occurred: Input files reference and features have incompatible contigs: Found contigs with the same name but different lengths:
    contig reference = chr1 / 248956422
    contig features = chr1 / 249250621..

    you know that I can not upload picture due to your website protection, I hope you can understand what I said
  • manbamanba Member
    > @AdelaideR said:
    > Hi @pwaltman I sent you a private message with some more information. The hg38 bundle is nearly complete, but not ready for release. I have sent instructions on how to use it in your workflow, the public release should be ready soon.

    so do you mean hg38 in your bundle is not able for production in present time, will the varaint change a lot if we use hg38, thanks a lot.
  • bhanuGandhambhanuGandham Member, Administrator, Broadie, Moderator admin

    Hi @manba

    Please try not posting the same questions in 2 threads, it then takes us twice as long to get to your answer.
    Lets tackle this issue here.

    Regards
    Bhanu

  • bhanuGandhambhanuGandham Member, Administrator, Broadie, Moderator admin
    edited December 4

    @manba

    so do you mean hg38 in your bundle is not able for production in present time.

    The hg38 files in the bundle are available for use to the public.

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