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Question about output vcf format of svict
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 :)