Collapsed Haplotype Pattern Method for Linkage Analysis of Next-Generation Sequencing Data
Project description
SEQLinkage
Collapsed Haplotype Pattern Method for Linkage Analysis of Next-Generation Sequencing Data
Pre-requisites
Make sure you install the pre-requisited before running seqlink:
conda install -c conda-forge xeus-cling
conda install -c anaconda swig
pip install egglib
git clone https://github.com/statgenetics/cstatgen.git
cd cstatgen
python setup.py install
Install
pip install SEQLinkage
How to use
1. Test on seqlinkage-example
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
2. Test on AD family
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
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