##fileformat=VCFv4.2
##NOTE=We split the RNC values with a comma where originally they are a 2-character string.
##FILTER=<ID=PASS,Description="All filters passed">
##GLnexusVersion=v1.4.1-0-g68e25e5
##GLnexusConfigName=/tmp/clair3.yml
##GLnexusConfigCRC32C=496041348
##GLnexusConfig={unifier_config: {drop_filtered: false, min_allele_copy_number: 1, min_AQ1: 10, min_AQ2: 10, min_GQ: 2, max_alleles_per_site: 32, monoallelic_sites_for_lost_alleles: true, preference: common}, genotyper_config: {revise_genotypes: true, min_assumed_allele_frequency: 9.99999975e-05, snv_prior_calibration: 1, indel_prior_calibration: 1, required_dp: 1, allow_partial_data: true, allele_dp_format: AD, ref_dp_format: MIN_DP, output_residuals: false, more_PL: true, squeeze: false, trim_uncalled_alleles: true, top_two_half_calls: false, output_format: BCF, liftover_fields: [{orig_names: [MIN_DP, DP], name: DP, description: "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">", type: int, number: basic, default_type: missing, count: 1, combi_method: min, ignore_non_variants: true}, {orig_names: [AD], name: AD, description: "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">", type: int, number: alleles, default_type: zero, count: 0, combi_method: min, ignore_non_variants: false}, {orig_names: [GQ], name: GQ, description: "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">", type: int, number: basic, default_type: missing, count: 1, combi_method: min, ignore_non_variants: true}, {orig_names: [PL], name: PL, description: "##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"Phred-scaled genotype Likelihoods\">", type: int, number: genotype, default_type: missing, count: 0, combi_method: missing, ignore_non_variants: true}]}}
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency estimate for each alternate allele">
##INFO=<ID=AQ,Number=A,Type=Integer,Description="Allele Quality score reflecting evidence for each alternate allele (Phred scale)">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##FILTER=<ID=MONOALLELIC,Description="Site represents one ALT allele in a region with multiple variants that could not be unified into non-overlapping multi-allelic sites">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=RNC,Number=2,Type=Character,Description="Reason for No Call in GT: . = n/a, M = Missing data, P = Partial data, I = gVCF input site is non-called, D = insufficient Depth of coverage, - = unrepresentable overlapping deletion, L = Lost/unrepresentable allele (other than deletion), U = multiple Unphased variants present, O = multiple Overlapping variants present, 1 = site is Monoallelic, no assertion about presence of REF or ALT allele">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype Likelihoods">
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##contig=<ID=3,length=198022430>
##contig=<ID=4,length=191154276>
##contig=<ID=5,length=180915260>
##contig=<ID=6,length=171115067>
##contig=<ID=7,length=159138663>
##contig=<ID=8,length=146364022>
##contig=<ID=9,length=141213431>
##contig=<ID=10,length=135534747>
##contig=<ID=11,length=135006516>
##contig=<ID=12,length=133851895>
##contig=<ID=13,length=115169878>
##contig=<ID=14,length=107349540>
##contig=<ID=15,length=102531392>
##contig=<ID=16,length=90354753>
##contig=<ID=17,length=81195210>
##contig=<ID=18,length=78077248>
##contig=<ID=19,length=59128983>
##contig=<ID=20,length=63025520>
##contig=<ID=21,length=48129895>
##contig=<ID=22,length=51304566>
##contig=<ID=X,length=155270560>
##contig=<ID=Y,length=59373566>
##bcftools_viewVersion=1.19+htslib-1.19.1
##bcftools_viewCommand=view test.bcf; Date=Thu Feb  8 15:26:01 2024
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE1	SAMPLE2
1	10108	1_10108_C_CT	C	CT	16	.	AF=0.5;AQ=16	GT:DP:AD:GQ:PL:RNC	./.:17:17,0:0:128,0,278:II	1/1:15:1,14:1:16,4,0:..
1	10109	1_10109_A_T	A	T	10	.	AF=0.25;AQ=10	GT:DP:AD:GQ:PL:RNC	0/1:11:7,3:9:10,0,25:..	0/0:15:15,0:44:0,45,449:..
1	10147	1_10147_C_CCCCTAA	C	CCCCTAA	24	.	AF=0.5;AQ=24	GT:DP:AD:GQ:PL:RNC	0/1:11:3,3:5:16,0,15:..	0/1:15:1,11:4:24,0,10:..
1	10206	1_10206_A_AC	A	AC	11	.	AF=0.25;AQ=11	GT:DP:AD:GQ:PL:RNC	./.:15:15,0:0:104,0,254:I,I	0/1:15:4,11:2:11,0,8:..
1	10212	1_10212_A_AC	A	AC	10	.	AF=0.25;AQ=10	GT:DP:AD:GQ:PL:RNC	./.:15:15,0:0:104,0,254:I,I	0/1:15:3,11:1:10,0,5:..
1	10218	1_10218_A_AC	A	AC	10	.	AF=0.25;AQ=10	GT:DP:AD:GQ:PL:RNC	./.:13:13,0:0:50,0,260:I,I	0/1:15:2,11:0:10,0,5:..
1	10230	1_10231_C_CCCTAA;1_10230_AC_A	AC	ACCCTAA,A	23	.	AF=0.5,0.25;AQ=19,23	GT:DP:AD:GQ:PL:RNC	1/2:11:.,3,6:5:0,0,0,0,0,0:..	0/1:15:2,11,0:2:19,0,8,990,990,990:..
1	10254	1_10254_T_C	T	C	26	.	AF=0.75;AQ=26	GT:DP:AD:GQ:PL:RNC	0/1:11:6,2:5:5,0,23:..	1/1:15:2,11:2:26,3,0:..
1	10257	1_10257_A_C	A	C	29	.	AF=0.75;AQ=29	GT:DP:AD:GQ:PL:RNC	0/1:11:6,4:4:7,0,7:..	1/1:15:3,11:2:29,3,0:..
1	10291	1_10291_C_T	C	T	27	.	AF=0.5;AQ=27	GT:DP:AD:GQ:PL:RNC	0/1:11:1,8:7:20,0,7:..	0/1:15:1,13:6:27,0,3:..