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tjiangHIT / cuteSV

Long read based human genomic structural variation detection with cuteSV
MIT License
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SV min_size ignored #118

Closed svenwillger closed 1 year ago

svenwillger commented 1 year ago

Hi @tjiangHIT,

I ran cuteSV twice on the same genome to check out the differences between my old version 1.0.11 and the latest version 2.0.2 and used the same settings: cuteSV -t 2 -S HG01258 --min_size 50 --genotype --max_cluster_bias_INS 1000 --diff_ratio_merging_INS 0.9 --max_cluster_bias_DEL 1000 --diff_ratio_merging_DEL 0.5 ... and was surprised to see that the new analysis resulted in 5-times more calls than the old version. After looking into the vcf file I realized that the "min_size" setting is ignored and all SVLEN are reported:

PRECISE;SVTYPE=INS;SVLEN=18;END=9200;CIPOS=-1,1;CILEN=-1,1;RE=43;RNAMES=NULL;AF=0.7414 PRECISE;SVTYPE=INS;SVLEN=47;END=33176;CIPOS=-0,0;CILEN=-1,1;RE=43;RNAMES=NULL;AF=0.4831 PRECISE;SVTYPE=INS;SVLEN=23;END=36389;CIPOS=-98,98;CILEN=-2,2;RE=47;RNAMES=NULL;AF=0.5802 PRECISE;SVTYPE=BND;RE=39;RNAMES=NULL;AF=1.0 PRECISE;SVTYPE=BND;RE=13;RNAMES=NULL;AF=1.0 PRECISE;SVTYPE=INS;SVLEN=46;END=2391;CIPOS=-1,1;CILEN=-1,1;RE=24;RNAMES=NULL;AF=0.5714 PRECISE;SVTYPE=INS;SVLEN=28;END=4918;CIPOS=-90,90;CILEN=-1,1;RE=27;RNAMES=NULL;AF=0.4909 PRECISE;SVTYPE=DEL;SVLEN=-12;END=11340;CIPOS=-1,1;CILEN=-0,0;RE=30;RNAMES=NULL;AF=0.3659;STRAND=+- PRECISE;SVTYPE=DEL;SVLEN=-18;END=15664;CIPOS=-2,2;CILEN=-1,1;RE=82;RNAMES=NULL;AF=0.82;STRAND=+- PRECISE;SVTYPE=DEL;SVLEN=-23;END=17420;CIPOS=-0,0;CILEN=-0,0;RE=30;RNAMES=NULL;AF=0.3261;STRAND=+- PRECISE;SVTYPE=INS;SVLEN=47;END=28417;CIPOS=-0,0;CILEN=-0,0;RE=11;RNAMES=NULL;AF=0.3056 PRECISE;SVTYPE=DEL;SVLEN=-32;END=29260;CIPOS=-3,3;CILEN=-1,1;RE=58;RNAMES=NULL;AF=0.9355;STRAND=+- PRECISE;SVTYPE=BND;RE=40;RNAMES=NULL;AF=0.4819 PRECISE;SVTYPE=BND;RE=90;RNAMES=NULL;AF=1.0 PRECISE;SVTYPE=INS;SVLEN=12;END=22532;CIPOS=-95,95;CILEN=-0,0;RE=35;RNAMES=NULL;AF=0.407 PRECISE;SVTYPE=DEL;SVLEN=-47;END=23068;CIPOS=-0,0;CILEN=-0,0;RE=33;RNAMES=NULL;AF=0.3882;STRAND=+- PRECISE;SVTYPE=INS;SVLEN=316;END=27088;CIPOS=-0,0;CILEN=-0,0;RE=17;RNAMES=NULL;AF=0.2787

Did I do anything wrong (e.g. order of options) or is this a real issue with cuteSV?

Thanks in advance! Best, Sven

svenwillger commented 1 year ago

I just found https://github.com/tjiangHIT/cuteSV/issues/110.

Sorry!