can't post any more due to "links"

Hello,
I was able to ask a detailed question with links previously, but now I get the "you have to be around longer to post links" message. Can someone verify me so I can resume posting?
Thanks
Joe

PS ironically: sorry for the spam, I didn't know where else to post this!

Best Answer

Answers

  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Hi @joe_whitney,

    Can you explain why you need to post links? You should be able to describe any GATK errors or questions without links. We've implemented a system to help reduce spam and this involves new users being unable to post links. What is the GATK/Picard question you have?

  • My question was referring to specific versions of GATK tools in specific WDLs published on github, and it's hard to be clear about versions and documentation without linking since there are many different scripts published in different repos.

    Here's the question with links stripped of URL protocol so it will let me post a comment:

    Hello,

    We've been testing published Broad "production" workflow for paired-end single sample alignment and variant calling github.com/gatk-workflows/gatk4-germline-snps-indels ("paired-end single sample alignment and variant calling"). The workflow in the "production" pipeline appears to use HaplotypeCaller from GATK 3.5 while using other components from GATK 4. There is a separately published pipeline here github.com/gatk-workflows/gatk4-germline-snps-indels that uses GATK 4's HaplotypeCaller. We have tried running the joint discovery pipeline using both the HC 3.5 and HC 4 gvcfs as inputs, using the default parameters provided in the repositories. However, the results appear to be almost indistinguishable when run on the NIST NA12878 reference sample.

    Is this expected? is the production pipelinegithub.com/gatk-workflows/broad-prod-wgs-germline-snps-indels/blob/master/PairedEndSingleSampleWf.wdl "production pipeline " indeed using HC 3.5? It appears so from the gvcf headers, but we expected larger differences between versions 3.5 and 4 due to changes in the model used.

    Including @SChaluvadi who has been cited as the "WDL" expert, hope this is appropriate.

    -Joe

  • Meanwhile I'm seeing other people post questions about specific WDLs and referring to specific commits by link, this seems necessary. I've seen another thread where someone was "verified" so they could post links and this is what I want.

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @joe_whitney

    I will transfer this thread to the firecloud/WDL foum and @SChaluvadi will help you out with it.

    Regards
    Bhanu

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin
    edited November 2018

    @joe_whitney
    The differences in the algorithm between HaplotypeCaller from GATK 3 and GATK 4 is different in that it was upgraded for greater efficiency and robustness and to introduce greater capability. Therefore, there will be small differences in your results. Here is a great description of GATK 4 and how it is different from GATK 3!

    As for being able to post links, I have checked and you are already a verified user and it seems that you are very very close to being able to post links again! If you find that you cannot do so in the near future, please reach out to me and I can work on finding you another solution. In the meantime, can you try using markdown to see if that works?

    Post edited by SChaluvadi on
  • Thanks for your reply @SChaluvadi. I still can't post links in markdown. A score of "5" appears next to my name, is there some threshold I'm waiting to get to?

  • I re-posted my actual question in the GATK forum since it belongs there.
    gatkforums.broadinstitute.org/gatk/discussion/13745/using-haplotypecaller-3-5-vs-haplotypecaller-4-0-joint-calling-large-cohorts/p1?new=1
    (still can't link :( )

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @joe_whitney
    The threshold to be able to post links is currently at 10 points and it looks like every comment you post gets you 2 points.

  • @Schaluvadi I don't think that's the case (if it were, I'd already have over 10 points). Usually these systems give you points for doing different types of interaction, not the same one repeatedly. I think I got another point (up to 6 now) for liking your previous answer.

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin
    edited November 2018

    @joe_whitney We are still looking into a way to get you link posting ability - just wanted to let you know we haven't forgotten you :) In the meantime, if you happen to get 10 points let us know!

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @joe_whitney Sorry that we have been unable to manually grant you more points due to high volumes of spam but hopefully you are able to get more points based on the activities listed in the above link. At this time, we will be closing this ticket but if the blog's information does not help please let us know.

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