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Sarah Bonnin

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Latest activity by Sarah Bonnin
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    Sarah Bonnin commented,

    Hi Pamela Bretscher, Thank you. I've tried several things and, apparently, the `-ERC GVCF` option was the issue. When I remove it, I get the annotation fields. Do you know why this is happening? Fr...

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    Sarah Bonnin commented,

    Hi Pamela, Thank you for your reply. Today I have tried to run HaplotypeCaller with the newest version of GATK (4.2.0.0). While I do get a VCF file, I unfortunately don't get the fields "QD" and "F...

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    Sarah Bonnin created a post,

    HaplotypeCaller with additional annotation?

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    HI all, I am trying to run HaplotypeCaller with the --annotation/-A parameter, but it doesn't work, so I'm obviously doing something wrong. I am running it on RNA-seq data. a) GATK version used: 4....

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    Sarah Bonnin commented,

    Hi Pamela, Please, do so, thank you! And sorry for posting to the wrong forum. Best

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    Sarah Bonnin created a post,

    vcf file for mm39 somewhere?

    Answered

    Hello, Where do I find a vcf file of known variants for the mm39 assembly? Is it available somewhere? I want to run the "RNAseq short variant discovery" pipeline on RNA-seq data that were already a...