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Ann W

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Latest activity by Ann W
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    Ann W commented,

    1. Community
    2. New User Advice
    3. GATK working, but -ERC command not found

    That was the issue! Thanks so much, Gen! For reference, here is the new bash script that worked.  #!/bin/bashlee=/pine/scr/a/n/anndo1/Lee_NatureGenetics_2017_Germlinealign_dir=$lee/bulk_alignHaplot...

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    Ann W created a post,

    GATK working, but -ERC command not found

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    1. Community
    2. New User Advice

    I am attempting to use HaplotypeCaller for the first time -yay! For every sample (blah_case_blah) passed to the below script, I get two output files (e.g., GBM9_R2.DNA.g.vcf.gz.tbi and GBM9_R2.DNA....

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