Raw VCF files in figshare.
VCF files submitted by each participant.
Standardized VCF files in figshare.
Reformatted standard VCF files for pipelines comparison for each participant.
FASTA alignments and pairwise SNP matrices in figshare.
Whole genome SNPs FASTA alignment and pairwise SNP counts matrix submitted by each participant.
Script to map files to figshare is here.
Consensus VCF in figshare
Consensus VCF including common variants of all datasets.
| ID | Institutes | SNP Caller |
|---|---|---|
| ds1-cfsan | A | CFSAN |
| ds2-gatk3 | B | GATK v3.6 - Haplotype Caller |
| ds3-gatk3 | C | GATK v3.7.9 - Haplotype Caller |
| ds4-gatk3 | D | GATK v3.7 - Unified Genotyper (NASP) |
| ds5-gatk3 | C | GATK v3.7.9 - Haplotype Caller |
| ds6-gatk3 | A | GATK v3.8.0 - ? |
| ds7-gatk4 | E | GATK v4.0.6 - Haplotype Caller |
| ds8-gatk4 | F | GATK v4.0.9 - Haplotype Caller |
| ds9-samtl | G | samtools v0.1.19 |
| ds10-samtl | H | samtools v0.1.18 (NASP) |
| ds11-samtrm | H | samtools v0.1.18 (NASP) |
| ds12-pilon | I | Pilon v1.9 |
| - | J | samtools v1.3.1/bcftools v1.3.1 |
| - | K | PathogenWatch |