Convert VCF4.1 to VCF4.2 using bcftools (preferrably)

Question

[nikitavlassenko]

I need to convert VCF4.1 to VCF4.2, and I am using bcftools. There is the method called convert but I am not sure how to use it to specify the output version:

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

If it is not possible with bcftools, then vcftools also have a method vcf-convert:

http://vcftools.sourceforge.net/perl_module.html#vcf-convert

But the command given is unclear:

zcat file.vcf.gz | vcf-convert -r reference.fa > out.vcf

How to specify the output version here?

I need to do such a conversion because the pipeline that I am trying to run is accepting only VCF4.2 but I need it to run VCF4.1 also:

• https://github.com/macarthur-lab/hail-elasticsearch-pipelines/blob/master/luigi_pipeline/seqr_loading.py
• https://discuss.hail.is/t/vcf4-1-is-hail-utils-hailexception-array-index-out-of-bounds/1232

[Ram]

Neither bcftools nor vcftools speaks of "conversion" between versions 4.1 and 4.2.

To use hail, you'll need to fix specific differences between the 4.1 and 4.2 versions, which are not addressed by most tools. See this post for more information: What is the difference between VCF specifications 4.1 and 4.2?

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[nikitavlassenko]

Ok, got it, thanks you!

[from the mountains]

doesn't this do exactly that in vcftools? https://github.com/vcftools/vcftools/blob/master/src/perl/vcf-convert