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

[John-Drake]

I am trying to liftover the 1000 genome genotype likelihood files. These files contain no genotype data (e.g. no GT field). Instead, they contain the genotype likelihood (e.g. GL Field).

Is bcftools +liftover able to liftover these files?

Below is the code:

./bcftools-1.20/bcftools +liftover --no-version -Ou /storage/enc/data_public/1000G/all_b37_original_files/ALL.chr22.phase3_bc_union.20130502.biallelic_svm_snps_indelsAF0.005_svs.gl.vcf.gz -- \
  -s GRCh37/human_g1k_v37.fasta \
  -f GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
  -c GRCh38/hg19ToHg38.over.chain.gz \
  --reject output.sites.reject.bcf \
  --reject-type b \
  --write-src | \
./bcftools-1.20/bcftools sort -o output.sites.hg38.bcf -Ob --write-index
./bcftools-1.20/bcftools: /usr/local/lib/libcurl.so.4: no version information available (required by ./bcftools-1.20/bcftools)
./bcftools-1.20/bcftools: /usr/local/lib/libcurl.so.4: no version information available (required by ./bcftools-1.20/bcftools)
Writing to /tmp/bcftools.NUekd2
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
[W::vcf_parse_info] INFO 'CIEND' is not defined in the header, assuming Type=String
[W::vcf_parse_info] INFO 'CIPOS' is not defined in the header, assuming Type=String
[W::vcf_parse_info] INFO 'END' is not defined in the header, assuming Type=String
[W::vcf_parse_info] INFO 'SVLEN' is not defined in the header, assuming Type=String
[W::vcf_parse_info] INFO 'SVTYPE' is not defined in the header, assuming Type=String
Warning: input VCF includes symbolic alleles that might not properly lift over
[E::main_plugin] Unchecked error (2), exiting
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
Error encountered while parsing the input
Cleaning

Everything works well with the genotype files (and the example using WGS data).

Thank you!