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fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering
MIT License
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Merge SV having position -1 #133

Open cagaser opened 4 years ago

cagaser commented 4 years ago

Hello,

I am a bit confused with a merged SV having a position -1. 

chr17_KI270729v1_random        -1      chr17_KI270729v1_random_395     C       <DEL>   .       PASS    SUPP=26;SUPP_VEC=111111111111111110111111111;SVLEN=-5508;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.6;CHR2=chr17_KI270729v1_random;END=-1;CIPOS=0,1074;CIEND=0,1822;STRANDS=+- GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO     0/1:010:468:0,0:+-:.:DEL:chr17_KI270729v1_random_454:NA:NA:chr17_KI270729v1_random_454-chr17_KI270729v1_random_922  0/1:010:3421:0,0:+-:.:DEL:chr17_KI270729v1_random_296:NA:NA:chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1       0/1:010:11355:0,0:+-:.,.:DEL,DEL:chr17_KI270729v1_random_1747:NA:NA:chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1,chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1     0/1:010:3329:0,0:+-:.,.:DEL,DEL:chr17_KI270729v1_random_1063:NA:NA:chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1,chr17_KI270729v1_random_1063-chr17_KI270729v1_random_1821  0/1:010:12019:0,0:+-:.,.:DEL,DEL:chr17_KI270729v1_random_1079:NA:NA:chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1,chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1     0/1:010:3432:0,0:+-:.,.:DEL,DEL:chr17_KI270729v1_random_304:NA:NA:chr17_KI270729v1_random_267-chr17_KI270729v1_random_948,chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1     0/1:010:4944:0,0:+-:.,.,.:DEL,DEL,DEL:chr17_KI270729v1_random_1073:NA:NA:chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1,chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1,chr17_KI270729v1_random_1073-chr17_KI270729v1_random_1820      0/1:010:3364:0,0:+-:.,.:DEL,DEL:chr17_KI270729v1_random_552:NA:NA:chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1,chr17_KI270729v1_random_552-chr17_KI270729v1_random_937     0/1:010:12712:0,0:+-:.:DEL:chr17_KI270729v1_random_1091:NA:NA:chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1     0/1:010:3386:0,0:+-:.,.:DEL,DEL:chr17_KI270729v1_random_1032:NA:NA:chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1,chr17_KI270729v1_random_1032-chr17_KI270729v1_random_1818  0/1:010:3331:0,0:+-:.,.:DEL,DEL:chr17_KI270729v1_random_395:NA:NA:chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1,chr17_KI270729v1_random_395-chr17_KI270729v1_random_948     0/1:010:11866:0,0:+-:.,.:DEL,DEL:chr17_KI270729v1_random_1099:NA:NA:chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1,chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1     0/1:010:3366:0,0:+-:.:DEL:chr17_KI270729v1_random_308:NA:NA:chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1   0/1:010:3345:0,0:+-:.:DEL:chr17_KI270729v1_random_279:NA:NA:chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1       0/1:010:4878:0,0:+-:.,.,.:DEL,DEL,DEL:chr17_KI270729v1_random_607:NA:NA:chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1,chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1,chr17_KI270729v1_random_607-chr17_KI270729v1_random_944 0/1:010:3327:0,0:+-:.:DEL:chr17_KI270729v1_random_300:NA:NA:chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1   0/1:010:3471:0,0:+-:.:DEL:chr17_KI270729v1_random_296:NA:NA:chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1   ./.:NaN:0:0,0:--:NaN:NaN:NaN:NAN:NAN:NAN        0/1:010:3439:0,0:+-:.:DEL:chr17_KI270729v1_random_272:NA:NA:chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1       0/1:010:11665:0,0:+-:.,.:DEL,DEL:chr17_KI270729v1_random_1224:NA:NA:chr17_KI270729v1_random_446-chr17_KI270729v1_random_946,chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1   0/1:010:4943:0,0:+-:.,.:DEL,DEL:chr17_KI270729v1_random_273:NA:NA:chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1,chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1       0/1:010:12707:0,0:+-:.,.,.:DEL,DEL,DEL:chr17_KI270729v1_random_274:NA:NA:chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1,chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1,chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1  ./.:010:3340:0,0:+-:.:DEL:chr17_KI270729v1_random_285:NA:NA:chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1   0/1:010:3389:0,0:+-:.,.:DEL,DEL:chr17_KI270729v1_random_287:NA:NA:chr17_KI270729v1_random_334-chr17_KI270729v1_random_937,chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1     0/1:010:4916:0,0:+-:.,.:DEL,DEL:chr17_KI270729v1_random_273:NA:NA:chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1,chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1       0/1:010:3342:0,0:+-:.,.:DEL,DEL:chr17_KI270729v1_random_1073:NA:NA:chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1,chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1      0/1:010:3457:0,0:+-:.:DEL:chr17_KI270729v1_random_290:NA:NA:chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1"

I did the following:

  1. Merged SVs from delly, mateclever, and manta for each sample (27 samples in total)
  2. For experimental purposes, we tried to merge again the output files from step 1.

Why do we get -1 as position? Take for example the second supporting sample with the following FORMAT: 0/1:010:3421:0,0:+-:.:DEL:chr17_KI270729v1_random_296:NA:NA:chr17_KI270729v1_random_-1-chr17_KI270729v1_random_-1 why is the coordinate -1? Looking at the original file of this sample: 

chr17_KI270729v1_random 296     chr17_KI270729v1_random_296     C       <DEL>   .       PASS    SUPP=1;SUPP_VEC=010;SVLEN=-3421;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.6;CHR2=chr17_KI270729v1_random;END=3717;CIPOS=0,0;CIEND=0,0;STRANDS=+-  GT      0/1

why is the corrdinate not chr17_KI270729v1_random_296-chr17_KI270729v1_random_3717 ?

Thank you very much in advance.

carolynzy commented 3 years ago

I noticed the same behavior in my data. The start position from other SV callers is one digit larger than the referred one in SURVIVOR. So if the start position is from 0 (including 0 in the SV) then the recorded position in SURVIVOR is -1(outside the range of SV) and then the length of the SVs will be consistent between SV callers and SURVIVOR. Maybe this is a systematic bias?