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fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering
MIT License
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SURVIVOR merge is resulting in a lot of missing data, can I treat them as 0/0? #216

Open qizhengyang2017 opened 1 month ago

qizhengyang2017 commented 1 month ago

My command is 

SURVIVOR merge vcfs.txt 0.1 0 1 0 0 100 svim-asm_variants.vcf

Below are some lines of the SURVIVOR output which I changed format using bcftools. I wonder if I can treat the ./. as reference genotype?

CHROM   POS ID  SVTYPE  SVLEN   CHR2    END ARJ AY  BAHC    BDR BEL CMiso   DHL92   DOYA    DUD ESL Harukei3    INB KRY NA  NUN NY  OHG PI161   PI164   PI414   PSR QME SAS TOG TVT VEP
Cpichr01    21925   PI414.svim_asm.DEL.1    DEL -319    Cpichr01    22244       1/1 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1 1/1 ./. 1/1 ./. ./. ./. ./.
Cpichr01    29663   NA.svim_asm.DEL.1   DEL -144    Cpichr01    29807       1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1
Cpichr01    40685   PI414.svim_asm.INS.1    INS 252 Cpichr01    40685       1/1 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1 ./. ./. ./. ./. ./. 1/1 ./. 1/1 ./. ./. ./. ./.
Cpichr01    40702   INB.svim_asm.INS.1  INS 329 Cpichr01    40702       ./. ./. ./. 1/1 ./. 1/1 ./. ./. ./. ./. 1/1 1/1 ./. ./. ./. 1/1 ./. ./. ./. ./. 1/1 ./. ./. ./. ./. 1/1
Cpichr01    86520   INB.svim_asm.INS.2  INS 9342    Cpichr01    86520       ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./.
Cpichr01    147143  VEP.svim_asm.INS.2  INS 3486    Cpichr01    147143      ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1
Cpichr01    150014  KRY.svim_asm.INS.1  INS 380 Cpichr01    150014      1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1
Cpichr01    246939  INB.svim_asm.INS.4  INS 167 Cpichr01    246939      1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 ./. 1/1 1/1 1/1 1/1
Cpichr01    246939  PI414.svim_asm.INS.3    INS 192 Cpichr01    246939      ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1 ./. ./. ./. ./. ./. ./.