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Question about output vcf format of svict #16

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xyw1 opened this issue Jan 20, 2020 · 0 comments
Open

Question about output vcf format of svict #16

xyw1 opened this issue Jan 20, 2020 · 0 comments

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@xyw1
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xyw1 commented Jan 20, 2020

Hi authors,
svict is a really fast tool of calling SVs,but I am a little confused about the format of the output vcf .
Here is an example, I do not understand what the MATE fusion means. In most cases, the 5th column of a BND mutation in a vcf file indicates its strand information, but in this vcf, there is an N. or .N in the line of the first MATE, and I do not know the orientation of the first MATE.

chr4    25665006        bnd_44_1        N       N.      .       TWO_BP  SVTYPE=BND;MATEID=bnd_44_2;CLUSTER=1;CONTIG=1;SUPPORT=7;
chr4    25665007        bnd_44_2        C       ]chr6:117337161]C       .       TWO_BP  SVTYPE=BND;MATEID=bnd_44_1;CLUSTER=1;CONTIG=1;SUPPORT=7;

In lumpy, there are also two continuous lines represents the same fusion, they are actually synonyms, because they are representing the same DNA fragment. But in svict cases, I do not know whether the two lines are synonyms (as in lumpy), or two DNA fragments generated by a reciprocal translocation?
Hope that I am clear when clarifying this question :)

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