##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##contig=<ID=22>
##bcftools_viewVersion=1.17-4-gfe98a6b+htslib-1.17-1-g70df047
##bcftools_viewCommand=view -G -Ob ../data/imputed_v2.0_b38_chr22.bgz; Date=Tue Feb 28 16:28:27 2023
##bcftools_viewCommand=view -Oz /well/ckb/users/aey472/projects/annotate_rsids/data/imputed_v2.0_b38_chr22_nosamples.bgz; Date=Tue Feb 28 16:45:06 2023
##VEP="v107" time="2023-02-28 16:47:53" cache="/well/ckb/users/aey472/data/homo_sapiens/107_GRCh38" ensembl-variation=107.ab78711 ensembl=107.5f39899 ensembl-funcgen=107.0fbd7d5 ensembl-io=107.a473894 1000genomes="phase3" COSMIC="95" ClinVar="202201" HGMD-PUBLIC="20204" assembly="GRCh38.p13" dbSNP="154" gencode="GENCODE 41" genebuild="2014-07" gnomADe="r2.1.1" gnomADg="v3.1.2" polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2"
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|VARIANT_CLASS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|MANE_SELECT|MANE_PLUS_CLINICAL|TSL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|UNIPROT_ISOFORM|GENE_PHENO|SIFT|PolyPhen|DOMAINS|miRNA|AF|AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_AF|gnomADe_AF|gnomADe_AFR_AF|gnomADe_AMR_AF|gnomADe_ASJ_AF|gnomADe_EAS_AF|gnomADe_FIN_AF|gnomADe_NFE_AF|gnomADe_OTH_AF|gnomADe_SAS_AF|gnomADg_AF|gnomADg_AFR_AF|gnomADg_AMI_AF|gnomADg_AMR_AF|gnomADg_ASJ_AF|gnomADg_EAS_AF|gnomADg_FIN_AF|gnomADg_MID_AF|gnomADg_NFE_AF|gnomADg_OTH_AF|gnomADg_SAS_AF|MAX_AF|MAX_AF_POPS|CLIN_SIG|SOMATIC|PHENO|PUBMED|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS">
##VEP-command-line='vep --input_file /well/ckb/users/aey472/projects/annotate_rsids/data/imputed_v2.0_b38_chr22_nosamples.vcf.gz --dir_cache /well/ckb/users/aey472/data --assembly GRCh38 -o ../output/imputed_v2.0_b38_chr22_annot.0Kb.vcf --force_overwrite --vcf --everything --offline --distance 0 --cache'
##bcftools_viewCommand=view /well/ckb/users/aey472/projects/vep_annotation/output/imputed_v2.0_b38_chr22_annot.0Kb.vcf.gz; Date=Thu Mar  2 16:16:48 2023
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
22      10510497        chr22:10510497:A:G      A       G       .       .       CSQ=G|intergenic_variant|MODIFIER|||||||||||||||rs1457915203||||SNV||||||||||||||||||||||||||||||||||3.319e-05|0|0|0|0|0.0003159|0|0|0|0|0|0.0003159|gnomADg_EAS|||||||||
22      10519134        chr22:10519134:TGATA:T  TGATA   T       .       .       CSQ=-|intergenic_variant|MODIFIER|||||||||||||||rs1188336707||||deletion||||||||||||||||||||||||||||||||||0.0001|0|0|0.0009699|0|0|0|0|4.753e-05|0|0|0.0009699|gnomADg_AMR|||||||||
22      10519402        chr22:10519402:T:G      T       G       .       .       CSQ=G|intergenic_variant|MODIFIER|||||||||||||||rs1193222075||||SNV||||||||||||||||||||||||||||||||||3.128e-05|0|0|0|0|0.000846|0|0|0|0|0|0.000846|gnomADg_EAS|||||||||
22      10519607        chr22:10519607:C:G      C       G       .       .       CSQ=G|intergenic_variant|MODIFIER|||||||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||||||||||
22      10525190        chr22:10525190:C:G      C       G       .       .       CSQ=G|intergenic_variant|MODIFIER|||||||||||||||rs1267940861||||SNV||||||||||||||||||||||||||||||||||2.493e-05|0|0|0|0|0.0006432|0|0|0|0|0|0.0006432|gnomADg_EAS|||||||||
22      10527415        chr22:10527415:C:T      C       T       .       .       CSQ=T|intergenic_variant|MODIFIER|||||||||||||||rs1321359077||||SNV||||||||||||||||||||||||||||||||||0|0||0|0|0|0|0|0|0|0|0|gnomADg_AFR&gnomADg_AMR&gnomADg_ASJ&gnomADg_EAS&gnomADg_FIN&gnomADg_MID&gnomADg_NFE&gnomADg_OTH&gnomADg_SAS|||||||||
22      10528424        chr22:10528424:G:A      G       A       .       .       CSQ=A|intergenic_variant|MODIFIER|||||||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||||||||||
22      10531285        chr22:10531285:A:T      A       T       .       .       CSQ=T|intergenic_variant|MODIFIER|||||||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||||||||||
22      10531362        chr22:10531362:AGATGAAAT:A      AGATGAAAT       A       .       .       CSQ=-|intergenic_variant|MODIFIER|||||||||||||||rs1279372490||||deletion||||||||||||||||||||||||||||||||||2.817e-05|6.702e-05|0|0|0|0|0|0|0|0|0|6.702e-05|gnomADg_AFR|||||||||

bcftools +split-vep -f '%CHROM\t%POS\n' -i 'Gene~"BRCA1"' -d test.vcf

bcftools +split-vep -f '%CHROM\t%POS\n'  -d test.vcf
22      10510497
22      10519134
22      10519402
22      10519607
22      10525190
22      10527415
22      10528424
22      10531285
22      10531362

bcftools 1.17-4-gfe98a6b
Using htslib 1.17-1-g70df047