--- title: SEQLinkage keywords: fastai sidebar: home_sidebar summary: "Collapsed Haplotype Pattern Method for Linkage Analysis of Next-Generation Sequencing Data" description: "Collapsed Haplotype Pattern Method for Linkage Analysis of Next-Generation Sequencing Data" nb_path: "nbs/index.ipynb" ---
pip install SEQLinkage
seqlink --fam seqlinkage-example.fam --vcf seqlinkage-example.vcf.gz -f MERLIN --output RMBPt8 --jobs 8
seqlink --fam seqlinkage-example.fam --vcf seqlinkage-example.vcf.gz -f MERLIN --output RMB0 --jobs 8 --bin 0
seqlink --fam seqlinkage-example.fam --vcf seqlinkage-example.vcf.gz -f MERLIN --output RMB1 --jobs 8 --bin 1
seqlink --fam seqlinkage-example.fam --vcf seqlinkage-example.vcf.gz --freq EVSEAAF -o LinkageAnalysis -K 0.001 --moi AR -W 0 -M 1 --theta-max 0.5 --theta-inc 0.05 -j 8 --run-linkage
seqlink --fam data/mwe_normal_fam.csv --vcf data/first1000snp_full_samples.vcf.gz -f LINKAGE --blueprint data/genemap.hg38.txt --freq AF -K 0.001 --moi AD -W 0 -M 1
seqlink --fam data/mwe_normal_fam.csv --vcf data/first1000snp_full_samples.vcf.gz -f MERLIN --blueprint data/genemap.hg38.txt --freq AF