sgrzegor

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sgrzegor
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Ann Arbor
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  • @Sheila Ahh okay. That makes sense, so i imagine this is due to the high duplication rate in our models genome? For processing large groups would either of these commands be more reliable in terms of accuracy and/or runtime? Thank you, Steve
  • @Sheila No worries about the delay. Do you mean you don't see the variant present at 17361797 in the HC output? That's the problem, in the raw reads it seems there is a SNP with roughly 40x coverage of the alternate allele, but haplotype caller see…
  • Hi Sheila, I submitted the bug report today, the file is called sgrzegor.tar.gz and should contain everything needed to replicate the error. Thank you, Steve
  • HC from the nightly build (GenomeAnalysisTK-nightly-2017-04-06-g34bd8a3) gave the same results in both default and GVCF modes. However, I tried both the nightly and the stable 3.7 with the region (-L) set to the 200 bp immediately surrounding the m…