Warning in bcftools when subsetting a VCF by variant ID

Question

[Mwangana]

I have successfully subset a VCF by variant ID after phasing and imputing using Beagle 5.5, however, I am getting the warning "[W::vcf_parse_info] INFO 'END' is not defined in the header, assuming Type=String" in the VCF.

How can I resolve this warning?

I ran the command below:

bcftools view -i'ID=@chr6_variantlist.txt' reheader_6_chrfixed_filtered_imputed.vcf.gz

Answer 1

[Pierre Lindenbaum]

bcftools view  reheader_6_chrfixed_filtered_imputed.vcf.gz |\
awk '/^#CHROM/ {printf("##INFO=<ID=END,Number=1,Type=Integer,Description=\"Stop position of the interval\">\n");} {print;}' |\
bcftools  view -i'ID=@chr6_variantlist.txt'

[Mwangana]

@Pierre Lindenbaum, this works perfectly well as it prints to the screen correctly but the error returns when I redirect it to a file:

  bcftools view  reheader_6_chrfixed_filtered_imputed.vcf.gz |awk '/^#CHROM/ {printf("##INFO= \<ID=END,Number=1,Type=Integer,Description=\"Stop position of the interval\">\n");} {print;}' | \ bcftools  view -i'ID=@chr6_variantlist.txt' > reheader_6_chrfixed_filtered_imputed_var_hr.vcf \
[W::vcf_parse_info] INFO 'END' is not defined in the header, assuming Type=String

[Pierre Lindenbaum]

the message comes from the first bcftools.

verify by running gunzip -c instead of bcftools

gunzip -c  reheader_6_chrfixed_filtered_imputed.vcf.gz  | awk ...

[Pierre Lindenbaum]

cross-posted: https://bioinformatics.stackexchange.com/questions/23393/