VCF file problem header - TASSEL 5

[Celia VI]

Hi,

I have a .vcf file that I have generated using TASSEL and I am trying to run further analysis on the file and I am seeing some problems with the header of the file.

When I run the following:

 bcftools stats 40555-123.vcf.gz > check.stats

It prints this:

[W::bcf_hdr_check_sanity] PL should be declared as Number=G

[W::vcf_parse_info] INFO 'QualityScore' is not defined in the header, assuming Type=String

I was wondering if it is possible to change the header of it I have to correct some flags while running TASSEL. I am trying to change the header with bcftools and it seems that it is not working.

bcftools head 40555-123.vcf.gz
[W::bcf_hdr_check_sanity] PL should be declared as Number=G
##fileformat=VCFv4.0
##FILTER=<ID=PASS,Description="All filters passed">
##Tassel=<ID=GenotypeTable,Version=5,Description="Reference allele is not known. The major allele was used as reference allele">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the reference and alternate alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
##FORMAT=<ID=PL,Number=.,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">

Thank you very much in advance.