Error while merging trio VCFs

[Sai]

Hello,

I am getting the following error while trying to merge trio VCFs using the solution you provided here https://www.biostars.org/p/329022/ 

When merging multiple samples the QUAL, FILTER, and INFO fields are taken from the first record at each position.

Error: Additional header line '##SAMPLE=<ID=BH10322_1,Sex->', Could not parse VCF header line

I would appreciate any help.

Here is my command

${rtg} vcfmerge {child}.vcf.gz ${mother}.vcf.gz ${father}.vcf.gz -a "##PEDIGREE=<Child=${child},Mother=${mother},Father=${father}>" -a "##SAMPLE<ID=${child},Sex-${sex}>" -o ${trioID}_trio.vcf.gz

Thanks,

Sairam

[Len Trigg]

On Mon, 20 May 2024 at 09:13, Sai <srbe...@gmail.com> wrote:

Error: Additional header line '##SAMPLE=<ID=BH10322_1,Sex->', Could not parse VCF header line

Here is my command

${rtg} vcfmerge {child}.vcf.gz ${mother}.vcf.gz ${father}.vcf.gz -a "##PEDIGREE=<Child=${child},Mother=${mother},Father=${father}>" -a "##SAMPLE<ID=${child},Sex-${sex}>" -o ${trioID}_trio.vcf.gz

Looks like there is a typo in the sex declaration where there is a "-" instead of a "=", that should be "##SAMPLE<ID=${child},Sex=${sex}>"

 

But also your output:

Error: Additional header line '##SAMPLE=<ID=BH10322_1,Sex->', Could not parse VCF header line

Indicates that the ${sex} variable was empty, where it should be MALE or FEMALE.

Cheers,
Len.

[Sai]

Thanks, Len!