Clinical SARS-CoV-2 Variant Calling scripts for Wouters et al., 2024.
- FASTQ Files For Each CHLA Patient are deposited under NCBI BioProject PRJNA1087511.
| Sample ID | Accession |
|---|---|
| HP28958 | SAMN40446131 |
| HP48587 | SAMN40446132 |
| HP28956 | SAMN40446133 |
| HP28957 | SAMN40446134 |
| HP28961 | SAMN40446135 |
| HP28960 | SAMN40446136 |
- Merged_PASS_complete_calls.vcf: Merged VCF for all isolates.
- merged_min11074.vcf: Merged VCF for all isolates excluding site 11074.
- vcf2pmatrix.py: Scripts for extracting variant call matrix from VCF.
- ratio.py: Scripts for calculating REF allele ratio from call matrix.
- variant_plot.R: Scripts for plotting frequency.
Viral genomic RNA was extracted, sequenced and subject variant calling using as previously described. Briefly, variants were called using the actic-ncov2019 medeka protocol against reference hCoV-19/Wuhan/WIV04/2019 (EPI_ISL_402124). Variants were manually instepcted against BAM files usig Integrated Genomics Viewer (v2.12.3) and Geneious Prime (2023.1.2 Build 2023-04-27). Resulting variant call files (VCFs) were indexed and merged using tabix (v1.17) and bcftools (v1.17). MergedVCFs were filtered for quality (QUAL ≥ 30) and mono-allelic variant calls. Allele frequency was calculated as the abundance of alternate allele reads over reference allele reads using vcf2pmatrix.py and ratio.py. A bi-allelic tandem repeat insertion variant at position 11,074 CT/CCT,C was removed due to visualization constraints and can be viewed in the: Merged_PASS_complete_calls.vcf. Variants were visualized using custom scripts and the pheatmap package (v1.0.12).