Bcftools how to add SNP type to the INFO field (DEL,INS,INV,DUP..)

Question

[Michal Nevo]

Hi,

I have a VCF file [Which I created with bcftools mpileup| bcftools call ] and I want to make sure that the Bcftools stats is showing me real statistics.

This is an example for one record, how can I know the snp type?

CACTIG010000004.1       235611  .       G       C       228.213 . VDB=0.0326236;SGB=-0.651104;RPBZ=-1.1619;MQBZ=2.82843;MQSBZ=-1.41421;BQBZ=-0.852803;SCBZ=-2.82843;FS=0;MQ0F=0;MQ=54;DP=219;DP4=25,34,103,47;ADF=4,4;ADR=5,2;AD=9,6;AN=30;AC=20     -GT:PL:DP:SP:ADF:ADR:AD  1/1:193,16,0:9:0:0,6:1,2:1,8    1/1:255,9,0:25:10:0,17:2,6:2,23 1/1:233,42,0:14:0:0,12:0,2:0,14 1/1:25     5,51,0:17:0:0,12:0,5:0,17       1/1:255,36,0:28:11:0,20:2,6:2,26 0/1:155,0,71:.:.:.:.:.  0/1:129,0,21:.:.:.:.:.  0/1:11  6,0,207:.:.:.:.:.       0/1:207,0,11:.:.:.:.:.  0/1:127,0,175:.:.:.:.:. 0/1:155,0,71:9:3:0,2:3,4:3,6    0/1:131,0,19:6:0:1,3:0,2:1,5  0/1:116,0,207:16:0:7,3:4,2:11,5 0/1:207,0,11:11:7:0,6:2,3:2,9   0/1:130,0,176:15:2:4,4:5,2:9,6

I have tried to create the BCF file unsuccessfully with the commands :

bcftools mpileup -q 30 -Q 1 --annotate **INFO/ID**,INFO/AD,INFO/ADF,INFO/ADR,FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP
bcftools mpileup -q 30 -Q 1 --annotate **INFO/SVTYPE**,INFO/AD,INFO/ADF,INFO/ADR,FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP

How do I add the ID=type TAG? or SVTYPE? Is there a way to add it to my vcf file?

I want this information:

I looked at bcftools annotate but I see I need to add the annotation from an external file..

Answer 1

[Istvan Albert]

You would need to run a program that is able to determine the effects of a variant, for example

Annotation for SV and CNV

annotating a vcf file containing Structural Variants

https://bioconductor.org/packages/devel/bioc/vignettes/StructuralVariantAnnotation/inst/doc/vignettes.html