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dellytools / delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
BSD 3-Clause "New" or "Revised" License
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WES #207

Closed tyyiyi closed 3 years ago

tyyiyi commented 4 years ago

Hello, I am currently performing structural variation detection with respect to the whole exome data of lung cancer tissues. Do you think my -x parameter should use the bed file of the non-exon region when calling SV?

tobiasrausch commented 4 years ago

You could or you intersect the SV results with coding regions.

tyyiyi commented 4 years ago

Does it mean that the two breakpoints of structural variation are within the exon region? Or is there only one breakpoint in it?

tobiasrausch commented 4 years ago

Ideally both breakpoints are within the targeted regions (usually a bit larger than the coding regions)

tyyiyi commented 4 years ago

What if there is only one breakpoint in the area? Is it not credible? I have requested SR support. a bit larger than the coding regions? 500bp?

tobiasrausch commented 4 years ago

I don't think there is a general answer to that, depends on the target enrichment if regions outside the targets are covered or not.

tyyiyi commented 4 years ago

Please take a look at the following record:

chr1 182727451 DEL00000173 T . PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.1;CHR2=chr1;END=182884459;PE=6;MAPQ=60;CT=3to5;CIPOS=-1,1; CIEND = -1,1; SRMAPQ = 60; INSLEN = 0; HOMLEN = 0; SR = 11; SRQ = 1; CONSENSUS = TCATAATAAGTATAATTTAAGTATTGGCTAATAATATGTCTGGAATGAAGACAATTTATGATGAATTTTGTTTTTTATGATTTGGAGTTTTTTAAGTTTGGGGCCATTATAAGTAGTTTTTTTTTTTAATATTAATGCTTAAGAAGTTAAATTTATTCTATAATGTGCCATGTGTGAAGTTGAGAGATAATGGTCTTTTT; CE = 1.71992; RDRATIO = 0.972111; SOMATIC GT: GL: GQ: FT: RCL: RC:RCR:CN:DR:DV:RR:RV 0/1:-39.5566,0,-103.455:10000:PASS:1611:11468:5515:3:33:6:31:14 0/0:0, -14.7425,-188.092:147:PASS:2099:15353:7175:3:54:0:49:0

The SV area here is chr1:182727451-182884459 And my target area is: chr1 182672761 182672881 chr1 182794345 182794465 chr1 182803674 182803794 chr1 182806098 182806218 chr1 182806218 182806338 chr1 182806338 182806458 ... chr1 182881583 182881703 chr1 182883133 182883253 chr1 182883253 182883373 chr1 182883517 182883637 chr1 182884592 182884712 chr1 182884712 182884832 So it seems that these two breakpoints are not in my target area. Is this mutation credible? why?

tobiasrausch commented 3 years ago

As stated multiple times, delly has only limited applicability to WES or targeted data. It has been designed for WGS data.