HovhannesSahakyan

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Username
HovhannesSahakyan
Location
Tartu, Estonia
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Location
Tartu, Estonia

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  • Dear @bshifaw and @bhanuGandham , Can't upload the file. After successful login it gives the following error "550 example_vcfs_hovhannes.tar.gz: Overwrite permission denied". Meanwhile I managed to get fastas. First, I follow @bshifaw '…
  • Thank you very much for your feedback! Yes, you are right. I am now in the second phase. I confirm that single sample VCF files are different for different samples, and the variant positions and substitutions are correct.
  • Dear @bshifaw , Thank you very much for your answer! I wrote in my previous post that SelectVariants now work with GATK 3.8.1. The bug was corrected with that version already. Nevertheless, I ran it with GATK4 as you mentioned. gatk --java-opti…
  • I have an update on this issue. With GATK version 3.8.1 this error is eliminated. Nevertheless, all different one-sample mtDNA vcf files convert into exactly the same fasta sequences. Here are the commands: java -Xmx4G -jarGenomeAnalysisTK.jar -T …
  • Hello guys, Did you find a solution for this issue?
  • (Quote) Hello Sheila, I wanted to do the same with mtDNA. While using your suggestions I get the following error: INFO 17:09:16,431 GenomeAnalysisEngine - Strictness is SILENT INFO 17:09:16,534 GenomeAnalysisEngine - Downsampling Settings: Meth…