SiyangLiu

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SiyangLiu
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Siyang Liu

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  • Hi Sheila, Thanks so much. I have read the four links through but I am afraid that they cannot resolve my questions. In https://www.broadinstitute.org/gatk/guide/article?id=4442, I tried two understandings of how you did with multi-allelic variant…
  • In case there may not be a documentation, could you tell me what the best way is to learn about the GATK method to call the multi-allelic variants?
  • Dear Geraldine, Since the new reference is out, we can see no reason why we would use the old reference. However, we cannot run GATK with the new reference. Liftover will necessarily introduce transition errors. Could you please help?
  • Hi Geraldine, What is the difference between hapmap_3.3.b37.vcf.gz and the hapmap3 tag snps. I find they contain similar number of snps. How do you select snps from hapmap3 to produce this file hapmap_3.3b37.vcf.gz? Thanks in advance!
  • Hi, I want to align the short reads in bam towards a set of alternative contigs by assembly which contains a set of variants. First I try SVAltAligner walker but it seems that the class path of this walker is not specified in the relevant pages and…
  • Hi, could you please tell me how to use GenerateAltAlleleFasta? I cannot find this module in the GenomeSTRIP packge (svtoolkit_1.04.1228.tar.gz) or in the GATK module.
  • Is GenomeSTRIP powerful in identification of other types of variants like insertions, inversions, translocations, etcs now? We know it is good at deletion detection and genotyping in 1000 genome Phase I analysis but we haven't seem the evaluation of…
  • The decoy bam doesn't seem to contain reads from the fragment library (correct me if I am wrong). Do you know where I can find the bam file for data from the fragment library? Thank you.