Table of contents

1. Usage
   1. A simple run
   2. The Variant Call Format output
   3. IBD segments
   4. IBD scaffold

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Usage

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A simple run

To simply run the THORIN tool on your cohort, we assume you already have the following files ready:

• data.group : a group file listing focal individuals and reference individuals
• data_chr20.bcf : a genotype file containing at least your focal and reference individuals
• data_chr20.unrelated_samples.bcf : a genotype file containing unrelated individuals
• chr20.b38.gmap.gz : a genetic map file in the correct genome built (can be found here)

CHR=20
GRP=data.group
IN=data_chr20.bcf
UNR=data_chr20.unrelated_samples.bcf
MAP=chr20.b38.gmap.gz
OUT=data_chr20.thorin.prob

./thorin_v1.2 -I ${IN} -H ${UNR} -M ${MAP} -R chr${CHR} -G ${GRP} -O ${OUT}

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The Variant Call Format output

For the output to be in .vcf.gz or .bcf format, simply add the desired extension to the output file name, such that:

CHR=20
GRP=data.group
IN=data_chr20.bcf
UNR=data_chr20.unrelated_samples.bcf
MAP=chr20.b38.gmap.gz
OUT=data_chr20.thorin.prob.bcf

./thorin_v1.2 -I ${IN} -H ${UNR} -M ${MAP} -R chr${CHR} -G ${GRP} -O ${OUT}

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IBD segments

To output IBD segments, use in addition the option --ibd :

CHR=20
GRP=data.group
IN=data_chr20.bcf
UNR=data_chr20.unrelated_samples.bcf
MAP=chr20.b38.gmap.gz
OUT=data_chr20.thorin.prob.bcf
OUT_SEG=data_chr20.thorin_segments.prob

./thorin_v1.2 -I ${IN} -H ${UNR} -M ${MAP} -R chr${CHR} -G ${GRP} -O ${OUT} --ibd ${OUT_SEG}

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IBD scaffold

To output the scaffold based on IBD probabilities, use the option --scaffold:

CHR=20
GRP=data.group
IN=data_chr20.bcf
UNR=data_chr20.unrelated_samples.bcf
MAP=chr20.b38.gmap.gz
OUT=data_chr20.thorin.prob.bcf
OUT_SCAF=data_chr20.thorin_scaffold.vcf.gz

./thorin_v1.2 -I ${IN} -H ${UNR} -M ${MAP} -R chr${CHR} -G ${GRP} -O ${OUT} --scaffold ${OUT_SCAF}