Skip to content

Latest commit

 

History

History
34 lines (27 loc) · 1.84 KB

README.md

File metadata and controls

34 lines (27 loc) · 1.84 KB

ISHAM raw and standardized VCF files

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.

Dataset and pipeline summary:

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