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 :)
Hi authors,
svictis 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.Nin the line of the first MATE, and I do not know the orientation of the first MATE.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 :)