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Protocol publication

[…] to maximize heterozygosity according to CEU HapMap genotypes []. Array-based genotypes were prepared for linkage analysis in the same way, using annotation files for the appropriate array., The two Perl scripts used to extract genotypes from VCF files and format them for linkage analysis are freely available on our website [], as is the annotation file for HapMap Phase II SNPs. Users may also download VCF files containing WES SNP genotypes for the four individuals described here (both for HapMap Phase II and genotyping array SNPs), as well as files containing genotyping array genotypes for comparison., Multipoint parametric linkage analysis using WES and array genotypes was performed using MERLIN []. A population disease allele frequency of 0.00001 was specified, along with a fully penetrant recessive (family A, family T) or dominant (family M) genetic model. LOD scores were estimated at positions spaced 0.3 cM apart, and CEU allele frequencies were used., SAMtools mpileup/bcftools was also used to detect variants from the reference sequence with the default setting of t = 0.001. Variants were annotated by ANNOVAR [] using the UCSC Known Gene annotation. For the purposes of filtering variants, linkage peaks were defined as the intervals in which the genome-wide maximum LOD score was obtained, plus 0.3 cM on either side., bp: base pair; HMM: hidden Markov model; MPS: massively parallel sequencing; SNP: single nucleotide polymorphism; VCF: variant call format; WES: whole exome sequencing; WGS: whole genome sequencing., KRS conceived of the study and performed all analyses described in the article. MB provided guidance and ideas. CJB wrote software tools. MSH, AES, and RJHS performed whole exome sequencing. MSH performed array-based SNP genotyping. RJHS, RJL, HN, GM and DJA collected families and […]

Pipeline specifications

Software tools Merlin, SAMtools, bcftools, ANNOVAR
Diseases Genetic Diseases, Inborn