Authors: Alejandra I. Romero-Morales, Anuj Rastogi, Hoor Temuri, Megan Rasmussen, Gregory Scott McElroy, Lawrence Hsu, Paula M. Almonacid, Bryan Millis, Navdeep S Chandel, Jean-Philippe Cartailler and Vivian Gama
Please cite: TBD
All raw data has been deposited via GEO:
- SRA accession: PRJNA626388 (A reviewer link is available upon request)
- Release date: 2020-08-01 (tentative until manuscript is accepted for publication)
SNP: Deliverable-1/01-Preprocessing/Input/all.samples.filtered.snp.nonsynonymous.ann.vcf
Indel: Deliverable-1/01-Preprocesing/Input/all.samples.filtered.indel.nonsynonymous.ann.vcf
Used snpSift to extract the columns in both the SNP and indel VCF files before downstream analysis:
SNP file:
java -jar SnpSift.jar extractFields all.samples.filtered.snp.nonsynonymous.ann.vcf CHROM POS ID REF ALT QUAL "ANN[0].ALLELE" "ANN[0].EFFECT" "ANN[0].IMPACT" "ANN[0].GENE" "ANN[0].GENEID" "ANN[0].FEATURE" "ANN[0].FEATUREID" "GEN[GM01503].GT" "GEN[GM03672].GT" "GEN[GM13411].GT" > snpEff_processed.vcf
Indel file:
java -jar SnpSift.jar extractFields all.samples.filtered.indel.nonsynonymous.ann.vcf CHROM POS ID REF ALT QUAL "ANN[0].ALLELE" "ANN[0].EFFECT" "ANN[0].IMPACT" "ANN[0].GENE" "ANN[0].GENEID" "ANN[0].FEATURE" "ANN[0].FEATUREID" "GEN[GM01503].GT" "GEN[GM03672].GT" "GEN[GM13411].GT" > snpEff_processed_indel.vcf
SNP: Deliverable-1/01-Preprocessing/Output/snpEff_processed.vcf
Indel: Deliverable-1/01-Preprocessing/Output/snpEff_processed_indel.vcf
Deliverable-1/02-GeneWiz_reproduce/Input/snpEff_processed.vcf
Deliverable-1/02-GeneWiz_reproduce/Input/snpEff_processed_indel.vcf
Deliverable-1/02-GeneWiz_reproduce/Input/ensembl_to_uniprot
Run Deliverable-1/02-GeneWiz_reproduce/Src/snpeff_reproduce_GeneWiz_Variant_Hit.R
Location: Deliverable-1/02-GeneWiz_reproduce/Output/
Items:
genewiz_report_snpeff_indel_Gr37.xlsx
and genewiz_report_snpeff_snp_Gr37.xlsx
- reproduction of the GeneWiz report from raw data
snpeff_indel_Gr37.xlsx
and snpeff_snp_Gr37.xlsx
- additional information CDS added on top of the genewiz report
snpeff-gr37-indel-full.csv
and snpeff-gr37-snp-full.csv
- Input data generated for other deliverable.
Deliverable-2/01-snp-indel-circular-plot/Input/snpeff-gr37-indel-full.csv
- Run
Deliverable-2/01-snp-indel-circular-plot/Src/biocircos.R
- Save plots.
Note - three genes manually using Inkscape 0.92. Ticks have been drawn in.
Gene Name | chrom | end | start |
---|---|---|---|
AC074212.3 | 19 | 46236509 | 46267792 |
AC012123.1 | 18 | 30354376 | 30349758 |
AC096644.1 | 1 | 220608023 | 220603286 |
Location: Deliverable-2/01-snp-indel-circular-plot/Output/
SVG formatted circular plot:indel_circosplot_final.svg
Deliverable-2/01-snp-indel-circular-plot/Input/snpeff-gr37-snp-full.csv
- Run
Deliverable-2/01-snp-indel-circular-plot/Src/biocircos.R
- Save plots.
Location: Deliverable-2/01-snp-indel-circular-plot/Output/
SVG formatted circular plot: snp_circosplot_final.svg
Deliverable-2/02-snp-circular-chromosome-mito-plot/Input/snpeff-gr37-snp-full.csv
Deliverable-2/02-snp-circular-chromosome-mito-plot/Input/color_ref.csv
Deliverable-2/02-snp-circular-chromosome-mito-plot/Input/crossref.csv
- Run
Deliverable-2/02-snp-circular-chromosome-mito-plot/Src/mito_circos.R
- Save plots
Location: Deliverable-2/02-snp-circular-chromosome-mito-plot/Output/
SVG formatted circular plot: mito_circoplot.svg