Azza Ahmed
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Activity overview
Latest activity by Azza Ahmed-
Azza Ahmed commented,
Thank you again for the quick fix. I’m happy to confirm FilterFunctotator now resolves such transcript issues gracefully, and the pipeline runs to completion successfully- producing expected output...
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Azza Ahmed commented,
Great! Thank you very much. I will experiment with it and get back to you.
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Azza Ahmed created a post,
FilterFuncotations Duplicate key error
AnsweredHello, I'm using the `FilterFuncotations` to process the output from the `Functotator` as per this WARP [pipeline](warp/AnnotationFiltration.wdl at cec97750e3819fd88ba382534aaede8e05ec52df · broadi...
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Azza Ahmed commented,
Great, thank you! I took another detour and realized it is possible to get statistics on the vcf from the `VariantsEval` command (with the same dbsnp file I have at hand now). I will leave it as su...
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Azza Ahmed commented,
I'm beginning to think it is actually something to do with the dbsnp file. I tried to use `CollectVariantCallingMetrics` on a vcf derived from the gvcf I used above (ie, after passing the gvcf file...
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Azza Ahmed commented,
Thank you Genevieve Brandt (she/her). I'm afraid changing the format does not really solve it. Below are my logs: ``` $ mv GCF_000001405.39_ucsc-genbank-chrs.gz GCF_000001405.39_ucsc-genbank-chrs.v...
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Azza Ahmed commented,
You are right, my dbsnp file is problematic. I'm a bit surprised since it worked fine in the BQSR stage upstream. I'm putting the logs from validation and obtaining the dbsnp file below, and I'd re...
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Azza Ahmed commented,
Hi Genevieve Brandt (she/her), Thank you for the prompt response! Yes, I do confirm the issue is persistent in the latest gatk version: ``` [Wed Oct 06 18:56:06 CEST 2021] picard.vcf.CollectVariant...
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Azza Ahmed commented,
Hi! I'm actually getting the same error (using gatk 4.2.1.0), only running with a gvcf file while setting INPUT_GVCF ture as below. While a lot of time is spent processing, no file is produced, and...
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Azza Ahmed commented,
Hello, Thank you for providing this tutorial. Would you kindly provide another link to the example data- perhaps on Google cloud or Terra? The ftp site is not working (I see it has been disabled as...