README.md

GCAT|Panel

R scripts to reproduce work from:

Valls-Margarit et al. GCAT|Panel, a comprehensive structural variant haplotype map of the Iberian population from high-coverage whole-genome sequencing. Submitted.

1 Logistic Regression Model (LRM)

Code to generate the LRM using in-silico data for SNVs Indels and each Structural Variant (SV) type (mid DEL: Deletions 30-150bp; DEL: Deletions; DUP: Duplications; INS: Insertions; INV: Inversions; TRA: Translocations).

2 Merge callers

Code to merge variant callers for each GCAT individual and variant type.

3 Merge samples

Code to merge all GCAT samples for each variant type.

4 Genotyping Duplications, Translocations and de novo insertions detected by Pindel

Code to genotype Duplications, Translocations and de novo insertions from Pindel calling.

Further in-silico description, files and results can be found in http://cg.bsc.es/GCAT_BSC_iberianpanel/ web.
GCAT haplotype panel and other sample information (genotypes) can be found in EGA, under accession number EGAS00001003018.