DELLY SNV detection output intrepetation
Entering edit mode
4.0 years ago
mks002 ▴ 220

Dear all, I have performed SNV calling on plasmodium samples. However I am facing some difficulty to interpreting certain fields. I wish to annotate this .vcf file further.

Here is an example from one of the .vcf file

Pf3D7_02_v3     903199  BND00000329     A       A]Pf3D7_01_v3:84434]    .       LowQual IMPRECISE;SVTYPE=BND;SVMETHOD=EMBL.DELLYv0.7.7;CHR2=Pf
3D7_01_v3;END=84434;PE=3;MAPQ=1;CT=3to3;CIPOS=-115,115;CIEND=-115,115     GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV   0/0:0,-9.17065,-38.1212:92:P
Pf3D7_03_v3     90256   INV00000039     A       <INV>   .       LowQual IMPRECISE;SVTYPE=INV;SVMETHOD=EMBL.DELLYv0.7.7;CHR2=Pf3D7_03_v3;END=90
384;PE=2;MAPQ=40;CT=5to5;CIPOS=-55,55;CIEND=-55,55        GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV   0/0:0,-0.927125,-97.7996:10:LowQual:2513:642
Pf3D7_03_v3     282969  DEL00000154     A       <DEL>   .       LowQual IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.7.7;CHR2=Pf3D7_03_v3;END=28
3430;PE=2;MAPQ=42;CT=3to5;CIPOS=-153,153;CIEND=-153,153   GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV   0/0:0,-6.04816,-184.599:60:PASS:13141:28020:
Pf3D7_03_v3     598312  INV00000040     T       <INV>   .       LowQual IMPRECISE;SVTYPE=INV;SVMETHOD=EMBL.DELLYv0.7.7;CHR2=Pf3D7_03_v3;END=598470;PE=2;MAPQ=36;CT=5to5;CIPOS=-236,236;CIEND=-236,236   GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV   0/0:0,-3.72035,-65.2937:37:PASS:5282:4380:3205:1:25:1:0:0

Here are my specific doubts

  1. CT=5to5,3to5,5to5,3to3 what do these correspond to?
  2. CIEND=-55,55 why are these values in negative value and positive value of the same number.
  3. I performed svprops to convert .vcf to .bed and then to perform annotation did a bed intersect with the gtf file. The difficulty arises in case of Interchromosomal translocations (represented by tag BND). Because the start field corresponds to the original chromosome and end corresponds to the end co-ordinates of the chromosome of translocation( correct if this point is not right). So how to annotate these translocation events?

4.How well does latest SNPeff annotates SVs?

Thanks for help!

SNP DELLY SNV genome • 2.8k views

Login before adding your answer.

Traffic: 1883 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6