Brian Wiley
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Activity overview
Latest activity by Brian Wiley-
Brian Wiley commented,
Genevieve Brandt (she/her) Am I able to access to see updates on the bug report as a viewer? No big deal if I cannot view it though :)
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Brian Wiley commented,
I am also seeing this as well for version 4.2.1.0. I will see if I can create bug report but it indicates to only do so if asked so let me know. I also get something like below for PGT:PID 0|1:272...
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Brian Wiley commented,
David Benjamin, do you think it would be possible for Broad to start documenting things like this and most of the tags in your VCF files. More like simple things not like the algorithm for cluster...
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Brian Wiley created a post,
Mutect2 calls long deletion with absolutely zero read support
AnsweredIf you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.2.1.0b) Exact command used: /gatk/gatk Mutect2 --java-options "-Xmx8g" -O $1 -R $2 -I $3 -tumor "$TUMOR" -I $4 -norma...
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Brian Wiley commented,
I get this error below and PAPI is NOT mentioned once in the logs. I have only seen people post this error and in addition with something to do with PAPI. Why do I only get this error? I am runn...
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Brian Wiley commented,
To Whom can we request that this file af-only-gnomad.hg38.vcf.gz be updated. It was created 4 years ago.
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Brian Wiley commented,
Confirming Mutect2 does not have AC and AN tag correct? Just the 4.2 specification for AD?
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Brian Wiley commented,
Mar Gonzàlez-Porta, sorry the @ didn't work from Firefox.
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Brian Wiley commented,
Thanks. @Mar Gonzàlez-Porta, can you advise how you applied to all chromosomes after running BQSR on the autosomes?
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Brian Wiley commented,
What does this mean "model_autosomes_apply_all" and "model_allosomes_apply_allosomes". Only search brings me back to this thread. Is this a param(s) in ApplyBQSR?