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

Question

[evelyn]

Hello,

I have made vcf files using platypus:

samtools view -bS example.sorted.bam > example_1.sorted.bam
samtools index example_1.sorted.bam
python Platypus.py callVariants --bamFiles=example_1.sorted.bam --refFile=ref.fa  --output=example.vcf

But I get the following when I try to merge the vcf files using bcftools merge:

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

I am not sure if I should be concerned with this or not. And how to solve this. Thank you for your help!

Answer 1

[WouterDeCoster]

It's a warning that the number of GL is incorrectly declared in the header, but that probably won't affect downstream analysis.