Workflow for COV mutation analysis

• Updated on: Feb 7, 2021

Haplotype pipeline

• Command interface:

 pick-iso-var.py --help
 export-vcf.py --help

• Show contries with 1000 or more genomes: pick-iso-var.py --topmost
• Export iso & var for a country:

pick-iso-var.py --country India # default sample size & var freq: at most 100 per month; at least 0.5% var frequency 
pick-iso-var.py --country India --freq_cut 0.01 # change minimum freq
pick-iso-var.py --country India --per_month 200 # change most number per month

• Filter on a locus: pick-iso-var.py --country India --locus S
• Filter on missense: pick-iso-var.py --country India --missense
• Combine options: pick-iso-var.py --country Inida --missense --locus S

Step 1. GISAID download, parsing into database, update browser

• Personnel: Edgar & Lia

• Tools: Python, Perl, SQL & JavaScripts

• Outputs:

  • Relational database populated
  • Genome browser updated

• Main tables & schema:

  • Annotation: human_anno; vgeo
  • Variants: cv_snp; cv_del; cv_ins
  • Genotype: acc_hap; hap_chg

Step 2. Export isolate EPIs & high-frequency variants (cutoff: derived allele frequency >= 0.1%)

• Personnel: Lily

• Tools:

  • export-maf.py <country name>

• Main queries:

select a.acc, a.col_date, b.area, b.country from human_anno a, vgeo b where a.need is true and a.geo_id=b.geo_id and a.acc != %s and a.acc != %s and b.country = %s order by col_date;`
select acc, chg from acc_hap a, hap_chg b where a.hid = b.hid and acc in %(l)s;

• Outputs:

  • iso.tsv (isolates, geo, collection dates)
  • var.tsv (variants with consequence calls and frequency/counts)

• TO DO:

  • implement command-line options (for continent & country)
  • standardize dates

Step 3. Export vcf.gz file

• Personnel: Weigang
• Script: export-vcf.py --iso <iso.tsv> --var <snp.tsv>
• Main queries:

select * from cv_snp where concat(alt, site) = %s;
select * from cv_del where del = %s;     
select * from cv_ins where ins = %s;
select acc, chg from acc_hap a, hap_chg b where a.hid = b.hid and acc in %(l)s;

• Outputs:
  • country.vcf (gzip to vcf.gz)

Step 4. Mutation analysis

• Personnel: Saymon, Lily & Desiree
• Scripts & tools: vcftools, bcftools, ldhat, hapview, TCS, RStudio
• Outputs:
  • time series of maf (> 1% in a country)
  • syn & nonsyn diversity (ps & ps) per gene
  • recombination analysis: linkage maps, ldhat, hapview
  • haplotype networks: TCS & tcsBU