SEQLinkage 1.0.2

Collapsed Haplotype Pattern Method for Linkage Analysis of Next-Generation Sequencing Data

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