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symlinks to bam files

tommycarstensentommycarstensen United KingdomMember ✭✭✭
edited August 2015 in Ask the GATK team

It's great that the GATK walkers can follow symlinks to bam files. But I've never understood, why GATK UG and HC can't look for the index file in the same location as the bam. Instead one has to also create symlinks to the index files in the same location as the symlinks to the bam files. This prevents one from using as input a file with bam symlinks. There are several ways to work around this, but it's just such an annoying obstacle, which I run into every 3 or 6 months, because I forget about this behaviour. Please please fix and you can come and raid my mini fridge at work full of chocolate (currently also holds LEGO). If you choose to ignore this enhancement request, then GATK is still a pretty good tool :)

If you have no clue what I'm talking about, then feel free to delete this ticket. It's just one of those small nuisances...

Tagged:

Issue · Github
by Geraldine_VdAuwera

Issue Number
781
State
open
Last Updated

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MA admin
    Accepted Answer

    You store LEGO in your fridge? You strange, strange man.

    Totally understand what you mean, but I'm afraid there's no way its going to happen in GATK3 unless someone external contributes a patch. However, I will pass on the suggestion to the GATK4 tiger team... (yeah it's a separate dev team at this point; long story that will become clearer in a month or two).

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Accepted Answer

    You store LEGO in your fridge? You strange, strange man.

    Totally understand what you mean, but I'm afraid there's no way its going to happen in GATK3 unless someone external contributes a patch. However, I will pass on the suggestion to the GATK4 tiger team... (yeah it's a separate dev team at this point; long story that will become clearer in a month or two).

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