search

fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering
MIT License
354 stars 47 forks source link

SURVIVOR wrong merge #91

Closed Litterlemon closed 5 years ago

Litterlemon commented 5 years ago

hello， some records going wrong when i use SURVIVOR to merge some vcf. Such as: 19 39898269 DEL001617805SUR N <DEL> . PASS SUPP=1;SUPP_VEC=01;AVGLEN=1075;SVTYPE=DEL;SVMETHOD=SURVIVORv2;CHR2=19;END=39898388;CIPOS=-956,0;CIEND=-956,0;STRANDS=+- GT:PSV:LN:DR:ST:TY:CO ./.:NaN:0:0,0:--:NaN:NaN 0/1:NA:1075:0,2:+-:DEL,DEL:19_39898269-19_39898388,19_39897313-19_39898388

19_39897313-19_39898388 is not exist in original vcf,but is

20 39897313 1089548 N <DEL> . PASS PRECISE;SVMETHOD=Snifflesv1.0.8;CHR2=20;END=39898388;STD_quant_start=0.000000;...

fritzsedlazeck commented 5 years ago

Hi, Thanks for reaching out. I don't quite understand the problem. The entry is exactly what you showed. It summarizes the start and the end coordinate with it's chromosome for both breakpoints. So I don't see the problem. Thanks Fritz

Litterlemon commented 5 years ago

hi,Fritz i don't understand why different chromosome were merged together.

fritzsedlazeck commented 5 years ago

Can you send me that VCF file? fritz.sedlazeck@gmail.com And please let me know what version of SURVIVOR you are using. Thanks Fritz