David Murphy
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Latest activity by David Murphy-
David Murphy commented,
Trying to rule out various possibilities I removed a few outlier samples that I thought might be the issue with extremely low reads but it had no effect and I continued to get the same error. This ...
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David Murphy created a post,
VariantRecalibrator throwing VariantRecalibratorEngine - Evaluate datum returned a NaN warning then crashing with empty tranches file.
I'm running a batch of 250 exomes. It crashes with the error below and and produces an empty tranches file. I don't *think* there's anything special about the samples in this batch but the other 49...
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David Murphy commented,
The links for method documentation, parameter recommendations and tutorial are all dead.
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David Murphy commented,
I tried to post another reply here about some other dead links but it just never turned up. I'm getting a lot of google links to the site that lead to SSL_ERROR_BAD_CERT_DOMAINhttps://gatkforums.br...
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David Murphy commented,
Thanks so much for the remarkably fast fix! I'll let you know if I hit any more but so far what I've tried has worked perfectly!
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David Murphy commented,
Have all the old tutorials and documentation been wiped out?User experience so far:Google "GATK4 haplotypecaller"First link: appears to be haplotypecaller Doc... redirects to front page. There's co...