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Shaun Clare

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Latest activity by Shaun Clare
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    Shaun Clare commented,

    1. Community
    2. General Discussion
    3. Cannot parallelize GATK

    I managed to fix it by modifying ls to write as one column using: ls -1 *.sorted.bam | <rest of command> I'm not sure why it worked in the first place, or maybe I accidentally deleted part of my co...

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    Shaun Clare created a post,

    Cannot parallelize GATK

    1. Community
    2. General Discussion

    So I am rather confused what is going on, I am trying to use HaplotyperCaller to genotype ~1100 samples. I ran this is exact code on the entire set, getting through ~800 when it was actively workin...

    • Shaun Clare
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    Shaun Clare commented,

    1. Community
    2. Special GATK Use Cases
    3. Issue with combining g.vcf files

    Unfortunately since its 44k separate amplicons, --merge-input-intervals wasn't able to work since it can't detect if they were abutting. I used --merge-contigs-into-num-partitions 50 instead and I ...

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    Shaun Clare commented,

    1. Community
    2. Special GATK Use Cases
    3. Issue with combining g.vcf files

    It seems to be working but I'm guessing this is going to take a long time. It got passed initializing the engine but gave a warning to not use more than 100 intervals, this uses 44,000 amplicons as...

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    Shaun Clare commented,

    1. Community
    2. Special GATK Use Cases
    3. Issue with combining g.vcf files

    Our pipeline was built using CombineGVCFs along time ago so I was familiar with it. Isn't the intervals option required to make the GenomicsDB datastore? I just want all SNP across the whole 'genome'

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    Shaun Clare created a post,

    Issue with combining g.vcf files

    Answered
    1. Community
    2. Special GATK Use Cases

    I have an issue with combining my g.vcfs. It is 96 samples called against an amplicon based reference so it's approximately 38k (called the 50k) sequences of 250 bp or less. These codes previously ...

    • Shaun Clare
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    Shaun Clare commented,

    1. Community
    2. Special GATK Use Cases
    3. CombineGVCFs

    I do have another issue on another project. This one uses the exact same codes but it's on 96 samples called against a much smaller amplicon based reference.  gatk CombineGVCFs --java-options "-Xmx...

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    Shaun Clare commented,

    1. Community
    2. Special GATK Use Cases
    3. CombineGVCFs

    Genevieve Brandt (she/her) Thank you, that seems to have worked!

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    Shaun Clare created a post,

    CombineGVCFs

    Answered
    1. Community
    2. Special GATK Use Cases

    So I noticed I was having trouble combining my g.vcf files, which is saying my index is out of bounds. My HaplotypeCaller command seemed to work fine and all of these codes work fine when I use amp...

    • Shaun Clare
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    Shaun Clare commented,

    1. Community
    2. New User Advice
    3. Invalid or corrupt jar file

    Running GATK worked fine and that code had worked previously. I couldn't find the error so I rebuilt my Ubuntu from scratch a while ago and it fixed everything so the code works again. Thanks, Shaun