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  • Thank you very much. I thought this would never happen .., but flexibility shows your strength.
  • Thank you. "the VCF record is completely superfluous as it's utterly obvious that a record represents an indel just by looking at it" Often we use script so it is not so obvious when we just want to grab them (grep/awk). Currently I just check th…
  • @ebanks said: Theoretically, it is (b). But we've stopped using the SB annotation because we never get goods results with it... Could you describe the problems of SB more detail? Is it related to false positive or false negative? I think…
  • As for using multiple methods, do VariantRecalibration and Base calibration any better than consensus of multiple methods, in particular an organism without any definitive SNP DB? I use 5 methods including GATK (no calibration), Mpileup, Freebayes, …
  • Hi Geraldine, It might not be the basic VCF specification. But other programs like Freebayes (BC), Mpileup (Heng) and Cortex (Zam), which I think are used in the 1000G, provide the information shown below. GATK may have different strategy than t…
  • Since I have real data of over 200 samples with aneuploidy, I can possibly write it if I know the guide line and some one can tell me which "section of programs of GATK" to check for this to start out. But does it needs to be in java? I can use java…
  • In a coming version, is it possible to GATK to automatically adjust ploidy value for each chromosome if a user provide the most abundant ploidy status? For reasonable samples, it is easy to determine ploidy value for a chromosome just from its media…
  • Thank you for the replies. So in principle, population analysis of Leishmania, which has extensive aneuploidy, does not make sense since a chromosome can have very different copy number among a population of parasites. Also, our experiments sugges…
  • Or more specifically, can we change ploidy setting for each chromosome while detecting variations?