Question: DELLY SNV detection output intrepetation
2
gravatar for mks002
2.4 years ago by
mks002190
Bangalore. India
mks002190 wrote:

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
ASS:12520:0:21281:0:48:0:0:0
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
2:3688:2:25:2:0:0
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:
14221:2:46:2:0:0
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!

snv delly snp genome • 1.8k views
ADD COMMENTlink written 2.4 years ago by mks002190
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