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Bug? Positions with reference values are listed as "Novel Variants"

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  • Sylvester
    I have just noticed that two of them were recently added to my novel-list(my bigY was done a year ago).
    And it looks like no INDELs in vcf:

    chrY 9879005 . C . 1484.13 PASS . GT 0
    chrY 14263127 . G . 103.184 PASS . GT 0

    Leave a comment:

  • wkauffman
    Look at the VCF file at that position to see if this is an INDEL (insertion or deletion).

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  • Bug? Positions with reference values are listed as "Novel Variants"

    I have noticed this bug in bigY results of kits that were done in August.
    Positions with reference or "?" values are listed as "Novel Variants".
    Is it correct? I think it is not.

    Please, check these positions:

    Position Ref Gen Conf //snp
    4902514 A ? Unknown L784 (A->T)
    7883549 G G High L800 (G->A)
    8684839 T T High L802 (T->C)
    9879005 C C High L858 (C->T)
    14028228 T T High L804 (T->A)
    14236879 A A High L791 (A->C)
    14263127 G G High L862 (G->T)
    15134176 G G High L808 (G->A)
    15668177 C C High L795 (C->T)
    16018726 C C High P321 (C->T)
    16699291 A A High L805 (A->G)
    17599534 T T High L803 (T->C)
    18146894 C C High L782 (C->G)
    18162467 G G High L793 (G->T)
    18180367 T T High L785 (T->C)
    21610585 C C High L968 (C->T)
    21779257 A A High --
    21898355 T T High --
    21900946 T T High L807 (T->G)
    22725125 C C High L790 (C->T)