Toy example
Table of contents
Rationale
We provided test files so that you understand the structure of command line options and verify that your code is running, especially if you compiled THORIN yourself on a different platform.
Toy example
Simply navigate in the folder test/ and run the following code (also provided in the bash script test/run.sh).
IN=related.chr20.vcf.gz
UNR=unrelated.chr20.vcf.gz
MAP=chr20.b37.gmap.gz
GRP=Trios.txt
OUT=test.prob
BIN=../bin/thorin_v1.2_static # change with your own version
./${BIN} -I ${IN} -H ${UNR} -M ${MAP} -R 20 -G ${GRP} -O ${OUT} --ibd ${OUT}.ibd --scaffold ${OUT}.ibd.scaffold.bcf
This code gives you 3 outputs:
- test.prob : the HMM IBD probability per variant site
- test.prob.ibd : the IBD segments and corresponding class (see documentation).
- test.prob.ibd.scaffold.bcf : the IBD-based scaffold in VCF/BCF format that you can use as input in the phasing software SHAPEIT5 to perform inter-chromosomal phasing.
If you want the probability per variant site in VCF/BCF format, you can simply add the suffix to the output file name, such as:
IN=related.chr20.vcf.gz
UNR=unrelated.chr20.vcf.gz
MAP=chr20.b37.gmap.gz
GRP=Trios.txt
OUT=test.prob.vcf.gz
BIN=../bin/thorin_v1.2_static # change with your own version
./${BIN} -I ${IN} -H ${UNR} -M ${MAP} -R 20 -G ${GRP} -O ${OUT} --ibd ${OUT}.ibd --scaffold ${OUT}.ibd.scaffold.bcf