Merge WGS .VCF files from multiple individuals into one .VCF file

Question

[lena.chan777]

Hello all,

I have WGS (whole genome sequencing) .vcf files for many samples, with each individual's WGS data saved in a single .vcf file. Could anyone give me some suggestions to combine all samples' .vcf files into one big .vcf file containing all samples? All suggestions are very welcome. Many thanks in advance.

PS. I've tried 'plink' and 'gatk -T CombineGVCFs', but neither of them work properly.

Best, Lena

Answer 1

[seraphya]

https://vcftools.github.io/perl_module.html#vcf-merge

http://samtools.github.io/bcftools/howtos/convert.html