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module load bio/BCFtools/1.11-GCC-10.2.0
for i in $(ls *.vcf.gz); do bcftools index --tbi $i; done
bcftools merge -Oz /work_directory/*.vcf.gz -o Merged.vcf.gz

2. Haplocheck

ContaminationHaplocheck detects in-sample contamination in mtDNA or WGS sequencing studies by analyzing the mitchondrial content. To run haplocheck, you can either use their cloud web service or install it locally.

wget https://github.com/genepi/haplocheck/releases/download/v1.3.3/haplocheck.zip
unzip haplocheck.zip
./haplocheck --out haplocheck_results Merged.vcf.gz 

3. Haplogrep

HaplogroupThe haplogroup classifications in Haplogrep are based on the revised tree by Dür et al, 2021, which is an update of the latest PhyloTree version 17 by van Oven, 2016 based on the work of van Oven & Kayser, 2009.

curl -sL haplogrep.now.sh | bash
./haplogrep classify --in Merged.vcf.gz --format vcf --out haplogroups_workshopsamples.txt

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txt

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4. Quality Control

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analysis 

The following files are going to be used for QC analysis: Merged.txt (raw variants data), haplocheck_results (contains the contamination status), andhaplogroups_workshopsamples.txt (contains the haplogroup information for each one of the samples).

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