Hi, I am trying to compare SVs obtained from assembly and mapping approaches and use survivor to switch from Assemblytics_structural_variants.bed to .vcf and then to the .bedpe format.
SURVIVOR is the only tool I've found that can translate and compare SVs and it works, thank you, I use it a lot.
However, I found that assemblytics tandem expansions are translated in a very strange way. For example, this variant
hpv16 1 6148 Assemblytics_b_3972 15093 + Tandem_expansion -6147 8946 tig00004375:14589-23535:+ between_alignments
was transformed into the vcf record
hpv16 1 Assemblytics_b_3972 N \ . LowQual IMPRECISE;SVTYPE=INS;SVMETHOD=Assemblytics;CHR2=hpv16;END=21241;SVLEN=21240;PE=1 GT 1/1
and then into
hpv16 2 2 hpv16 21242 21242 Assemblytics_b_3972 , + - INS
in bedpe notation,
where chr2 coordinate is located outside of the actual chromosome length (~8kb).
I am not sure whether we can translate tandem expansions into vcf in a way that allows us to compare them to sniffles SV's, but this one definitely wouldn't match anyway.
Hi, I am trying to compare SVs obtained from assembly and mapping approaches and use survivor to switch from Assemblytics_structural_variants.bed to .vcf and then to the .bedpe format. SURVIVOR is the only tool I've found that can translate and compare SVs and it works, thank you, I use it a lot. However, I found that assemblytics tandem expansions are translated in a very strange way. For example, this variant hpv16 1 6148 Assemblytics_b_3972 15093 + Tandem_expansion -6147 8946 tig00004375:14589-23535:+ between_alignments
was transformed into the vcf record hpv16 1 Assemblytics_b_3972 N \ . LowQual IMPRECISE;SVTYPE=INS;SVMETHOD=Assemblytics;CHR2=hpv16;END=21241;SVLEN=21240;PE=1 GT 1/1 and then into hpv16 2 2 hpv16 21242 21242 Assemblytics_b_3972 , + - INS in bedpe notation, where chr2 coordinate is located outside of the actual chromosome length (~8kb). I am not sure whether we can translate tandem expansions into vcf in a way that allows us to compare them to sniffles SV's, but this one definitely wouldn't match anyway.