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gubrins

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Latest activity by gubrins
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    gubrins commented,

    Heys again, You're right, the GVCF does not have a quality for the non-variant sites, but I was talking about the final vcf, after performing GenotypeGVCFs. If I do it with the functions from GATK ...

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    gubrins commented,

    Heys Genevieve-Brandt-she-her  thanks for your answer and thanks for pointing out the RGQ and GQ. However, my problem still continues, as the homozygous reference sites does not have any quality, a...

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    gubrins commented,

    Heys again Benjamin,  I am still getting that error and in later stages I don't have quality for the non-variant sites. Do you think this is affecting it?  

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    gubrins created a post,

    Not quality in invariant sites

    Answered

    If you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.1.7.0 b) Exact command used: HaplotypeCaller, CombineGVCFs, GenotypeGVCFsc) Entire error log: there is no error logIf ...

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    gubrins commented,

    Is a pity that nobody answered this question, I also want to create a know-site VCF file and I'm not really sure how to do it. Did you find out Haley Arnold?

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    gubrins commented,

    Thank you very much, I'm new with GATK and I appreacite the help! I'm planning to merge all my GVCF files and then run the GenotypeGVCF function, so I can get a merged VCF for all my samples.  I ha...

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    gubrins commented,

    Heys Linda, I also had some problems with the PATH. When you are trying this: ./gatk --help are you sure you are in that specific folder? If you do ls you should obtain gatk among others.  In order...

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    gubrins created a post,

    StrandBiasBySample error Haplotypecaller

    Good afternoon, I'm using GATK 4.1.7.0 and I'm trying to apply the Haplotypecaller function to a bam file. I was following mainly this post (https://gatk.broadinstitute.org/hc/en-us/articles/360039...