Construction of circos plot from WGS data

Question

[Anitha]

Hello everyone, As I am trying to construct a circos plot from the WGS data. I am struggling to organize the data like which data should be given as a input (SNV, CNV, SV). I have all these data in hand but having confusion which data to be used for the circos plot construction and how to organize that data to get a meaning full visualization.

Answer 1

[marco.barr]

Hi Anitha, you can take inspiration from here on which data to use and how to set up your WGS circle plot.
https://www.tandfonline.com/doi/full/10.1080/15384047.2018.1491498 Figure 2 seems consistent with your inputs. You could use circlize, I use it to build mtDNA graphs. It's great

[Anitha]

Thank you for the information. But, I am still struggling like which data to use and how to process the input data to represent to build the circos plot, How to link?? I am using circos command line tool. In that there are many input files were used to for the construction (karyotype.txt, ticks.txt, ideogram.txt, links.txt, histogram.txt, circos.config ... ect). In the link and histogram input file how do i need to process or organize the data and which data (like SNV, CNV and SV).

For example : This is my CNV and SNV data, How do i need to represent in the input file to make a circos plot

CNV Data :

1 121650000 125050000 3 gain

2 92150000 94200000 3 gain

3 90400000 91300000 3 gain

3 91500000 93450000 3 gain

3 93450000 93500000 1 loss

SNV Data:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample

chr1 10146 . AC A 165.92 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.465;DP=12;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.09;MQRankSum=1.465;QD=23.70;ReadPosRankSum=-1.465;SOR=0.223;ANNOVAR_DATE=2020-06-08;Func.refGene=intergenic;Gene.refGene=NONE\x3bDDX11L1;GeneDetail.refGene=dist\x3dNONE\x3bdist\x3d1727;ExonicFunc.refGene=.;AAChange.refGene=.;cytoBand=1p36.33;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;avsnp147=rs779258992;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;DANN_score=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_pred=.;MetaSVM_score=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_pred=.;integrated_fitCons_score=.;integrated_confidence_value=.;GERP++_RS=.;phyloP7way_vertebrate=.;phyloP20way_mammalian=.;phastCons7way_vertebrate=.;phastCons20way_mammalian=.;SiPhy_29way_logOdds=.;ALLELE_END GT:AD:DP:GQ:PL 1/1:1,6:7:15:180,15,0 chr1 13868 . A G 113.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.553;DP=24;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.31;MQRankSum=-2.091;QD=4.73;ReadPosRankSum=-0.445;SOR=0.941;ANNOVAR_DATE=2020-06-08;Func.refGene=ncRNA_exonic;Gene.refGene=DDX11L1;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;cytoBand=1p36.33;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;avsnp147=rs796086906;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;DANN_score=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_pred=.;MetaSVM_score=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_pred=.;integrated_fitCons_score=.;integrated_confidence_value=.;GERP++_RS=.;phyloP7way_vertebrate=.;phyloP20way_mammalian=.;phastCons7way_vertebrate=.;phastCons20way_mammalian=.;SiPhy_29way_logOdds=.;ALLELE_END GT:AD:DP:GQ:PL 0/1:17,7:24:99:121,0,385 chr1 14464 . A T 317.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.986;DP=40;ExcessHet=0.0000;FS=10.357;MLEAC=1;MLEAF=0.500;MQ=34.98;MQRankSum=0.931;QD=7.94;ReadPosRankSum=0.071;SOR=2.277;ANNOVAR_DATE=2020-06-08;Func.refGene=ncRNA_exonic;Gene.refGene=WASH7P;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;cytoBand=1p36.33;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;avsnp147=rs546169444;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;DANN_score=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_pred=.;MetaSVM_score=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_pred=.;integrated_fitCons_score=.;integrated_confidence_value=.;GERP++_RS=.;phyloP7way_vertebrate=.;phyloP20way_mammalian=.;phastCons7way_vertebrate=.;phastCons20way_mammalian=.;SiPhy_29way_logOdds=.;ALLELE_END GT:AD:DP:GQ:PL 0/1:26,14:40:99:325,0,674