Kaina Millan
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Activity overview
Latest activity by Kaina Millan-
Kaina Millan created a post,
SortVcf vs. MergeVcfs
Hello, I have a general question regarding the difference between MergeVcfs and SortVcf. From my understanding, after reading the documentation, they both work similarly? Both tools can accept more...
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Kaina Millan commented,
Thank you again!
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Kaina Millan commented,
Thank you so much for your quick response! Would you be able to notify me once the issue is fixed?
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Kaina Millan created a post,
FuncotatorDataSourceDownloader: Requester Pays
Hello, I was attempting to use FuncotatorDataSourceDownloader to acquire the germline datasource, but it looks like we now have to pay to acquire these resources. Is this correct? I wanted to ensur...
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Kaina Millan commented,
I will go ahead and give this a try- thank you so much for your help!
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Kaina Millan created a post,
Generating COSMIC.db Data Source for Funcotator
Hello, I am currently using Funcotator's (GATK4.6.1) v1.8 data source to annotate somatic variants after using Mutect2. I noticed that the COSMIC data source is v98, while the COSMIC site current...
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Kaina Millan commented,
Hello, I am wondering if a fix ended up being posted to your DataSources? I am having this same issue and was wondering how to work around it. I attempted using bcftools annotate as a temporary fix...
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Kaina Millan commented,
I appreciate you getting back to me! I am relatively new to WES, would you be able to provide an example when keeping calls from decoys would be necessary/useful for germline variant calling? In ad...
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Kaina Millan commented,
I just tried using Funcotator with hg38-v0-GRCh38.primary_assembly.genome.fa from GATK's resource bundle and that failed from the very start due to incompatible contigs: A USER ERROR has occurred: ...
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Kaina Millan commented,
I'd also like to add that half of my data ran perfectly fine. Tool returned "true" and there was no indication of the job failing while this second half of the data (second batch of cohorts) is giv...