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fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering
MIT License
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Invalid END? #159

Open bbimber opened 2 years ago

bbimber commented 2 years ago

Hello,

I ran cuteSV individually on samples, and then "SURVIVOR merge" on these. When I try to tabix sort the end product, I get this error:

+ /home/exacloud/gscratch/prime-seq/bin/tabix -p vcf -f cuteSV.vulcan.genotype.merged.vcf.gz
[E::hts_idx_push] Invalid record on sequence #1: end 16854370 < begin 31760131
tbx_index_build failed: cuteSV.vulcan.genotype.merged.vcf.gz

I originally posted this question on the cuteSV repo and their belief is that SURVIVOR is adding the END annotation. Do you have thoughts on this, and/or would other information help?

1       31760131        cuteSV.BND.17   N       N[5:16854370[   .       PASS    SUPP=12;SUPP_VEC=111111111111;SVLEN=0;SVTYPE=TRA;SVMETHOD=SURVIVOR1.0.7;CHR2=5;END=16854370;CIPOS=0,0;CIEND=0,0;STRANDS=++  GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO     0/0:NA:14905761:40,10:++:.:TRA:cuteSV.BND.17:NA:NA:1_31760131-5_16854370        ./.:NA:14905761:0,0:++:.:TRA:cuteSV.BND.17:NA:NA:1_31760131-5_16854370      0/0:NA:14905761:52,13:++:.:TRA:cuteSV.BND.17:NA:NA:1_31760131-5_16854370        ./.:NA:14905761:0,0:++:.:TRA:cuteSV.BND.17:NA:NA:1_31760131-5_16854370      ./.:NA:14905761:0,0:++:.:TRA:cuteSV.BND.17:NA:NA:1_31760131-5_16854370  0/0:NA:14905761:60,15:++:.:TRA:cuteSV.BND.17:NA:NA:1_31760131-5_16854370    0/0:NA:14905761:48,12:++:.:TRA:cuteSV.BND.17:NA:NA:1_31760131-5_16854370        ./.:NA:14905761:0,0:++:.:TRA:cuteSV.BND.17:NA:NA:1_31760131-5_16854370  ./.:NA:14905761:0,0:++:.:TRA:cuteSV.BND.17:NA:NA:1_31760131-5_16854370      ./.:NA:14905761:0,0:++:.:TRA:cuteSV.BND.17:NA:NA:1_31760131-5_16854370  ./.:NA:14905761:0,0:++:.:TRA:cuteSV.BND.17:NA:NA:1_31760131-5_16854370      ./.:NA:14905761:0,0:++:.:TRA:cuteSV.BND.17:NA:NA:1_31760131-5_16854370