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Goran Rakocevic

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Latest activity by Goran Rakocevic
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    Goran Rakocevic commented,

    1. Community
    2. Germline
    3. gvcf in Dragen mode and GenomicsDBImport

    Hi Gökalp Çelik Thanks!  I'm actually hoping to get both known sites and regular active site detection results, I thought that's what passing in alleles did? I'm calling a number lower coverage gen...

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    • Goran Rakocevic
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    Goran Rakocevic created a post,

    gvcf in Dragen mode and GenomicsDBImport

    1. Community
    2. Germline

    Hi, I'm running HC in Dragen mode (using broadinstitute/gatk:4.6.1.0 docker image): gatk --java-option -Xmx4g HaplotypeCaller \    -R <reference> \    -I <input_bam> \    -O <output_gvcf> \    --dr...

    • Goran Rakocevic
    • 2 followers
    • 3 comments
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    Goran Rakocevic commented,

    1. Community
    2. General Discussion
    3. Low coverage WGS data

    Hi Laura Gauthier Thanks! I didn't mean to shove 15,000 BAMs into a single HC call. I was thinking of maybe doing random batches of 50 or so...  That will cause batch effects, just wondering if tha...

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    Goran Rakocevic created a post,

    Low coverage WGS data

    1. Community
    2. General Discussion

    Hi All,   I'll be looking at calling variants on a cohort of ~15,000 low coverage genomes (1-2x).  I searched the forums and found that the recommendation is to use the regular best practices in t...

    • Goran Rakocevic
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    • 3 comments
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