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The location of the VCF files in the consgenome pipeline can be found at:

cd /results/variantcalling/

Merging multiple VCF files

We will use 'bcftools' to merge VCF files. Initially, we need to create a list of VCF files that we plan to merge. For example: while in the above directory do the following:

for i in `ls --color=never *.vcf`; do echo $i; echo $i >> file_list.txt; done

if you do not yet have 'bcftools' installed then run the following command to install it using conda

conda install -c bioconda bcftools

Now let’s create an index file for each VCF file:

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bcftools merge -l file_list.txt -0 -Oz -o merged_ALL.vcf.gz

uncompress version of merged vcf

bcftools merge -l file_list.txt -0  -o merged_ALL.vcf

Visualising the merged VCF file in IGV

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