GATK CNV germline plot vcf results

Question

[cocchi.e89]

I am working on some CNV analysis in human WGS samples through GATK CNV germline pipeline. I was wondering if there is any easy method to plot these results (I know they integrated it in the somatic CNV pipeline).

Here an example of the results .vcf:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  KO0002
1   3769201 CNV_1_3769201_4137300   N   .   3076.53 .   END=4137300 GT:CN:NP:QA:QS:QSE:QSS  0:2:332:20:3077:60:68
1   4137301 CNV_1_4137301_4137600   N   <DEL>   141.48  .   END=4137600 GT:CN:NP:QA:QS:QSE:QSS  1:0:1:141:141:141:141
1   4137601 CNV_1_4137601_6065700   N   .   3076.53 .   END=6065700 GT:CN:NP:QA:QS:QSE:QSS  0:2:3640:35:3077:12:83
1   6066301 CNV_1_6066301_6066600   N   <DEL>   11.88   .   END=6066600 GT:CN:NP:QA:QS:QSE:QSS  1:1:1:12:12:12:12
1   6066601 CNV_1_6066601_7174800   N   .   3076.53 .   END=7174800 GT:CN:NP:QA:QS:QSE:QSS  0:2:3166:24:3077:93:12
1   7174801 CNV_1_7174801_7175400   N   <DEL>   250.05  .   END=7175400 GT:CN:NP:QA:QS:QSE:QSS  1:0:2:154:250:135:193
1   7175401 CNV_1_7175401_7924500   N   .   3076.53 .   END=7924500 GT:CN:NP:QA:QS:QSE:QSS  0:2:1950:41:3077:15:41
1   7924801 CNV_1_7924801_7925100   N   <DEL>   14.91   .   END=7925100 GT:CN:NP:QA:QS:QSE:QSS  1:1:1:15:15:15:15
1   7925101 CNV_1_7925101_7925400   N   <DEL>   105.35  .   END=7925400 GT:CN:NP:QA:QS:QSE:QSS  1:0:1:105:105:105:105
1   7925401 CNV_1_7925401_10482600  N   .   3076.53 .   END=10482600    GT:CN:NP:QA:QS:QSE:QSS  0:2:5983:11:3077:11:88
1   10482601    CNV_1_10482601_10483500 N   <DEL>   73.13   .   END=10483500    GT:CN:NP:QA:QS:QSE:QSS  1:1:3:23:73:4:11
1   10483501    CNV_1_10483501_12835800 N   .   3076.53 .   END=12835800    GT:CN:NP:QA:QS:QSE:QSS  0:2:5245:4:3077:102:4

Thank you so much in advance for any help!

[newbio17]

Have you checked out the gCNV-related tutorials on GATK? You may want to check out this one which shows you some post-gCNV data conversions which you may need to visualize your data.