##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20160603
##source=consensus-genotypes-10X-freebayes.py
##commandline="(whatshap 0.12+61.gc9d9c22) phase --indels --distrust-genotypes --output-read-list whatshap/consensus/pacbioblasr/single/SH032.chr22.used-reads.tsv --changed-genotype-list whatshap/consensus/pacbioblasr/single/SH032.chr22.genotype-changes.tsv --reference ref/GRCh38_full_analysis_set_plus_decoy_hla.fa -o whatshap/consensus/pacbioblasr/single/SH032.chr22.vcf consensus/freebayes_10X/SH032.chr22.vcf pacbio/HG00512.chr22.bam pacbio/HG00513.chr22.bam pacbio/HG00514.chr22.bam"
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phase set identifier">
##contig=<ID=chr22>
##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">
##bcftools_viewVersion=1.6+htslib-1.6
##bcftools_viewCommand=view -s HG00514 --phased vcf/HG00514.chr22.tmp.vcf.gz; Date=Tue Jul 17 15:11:30 2018
##bcftools_mergeVersion=1.6+htslib-1.6
##bcftools_mergeCommand=merge --missing-to-ref vcf/HG00514.chr22.vcf.gz vcf/NA19240.chr22.vcf.gz; Date=Tue Jul 17 16:20:29 2018
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample1	sample2
chr21	10558266	.	G	A	.	.	AN=4;AC=0	GT:PS	0/0/0/0:.	0|0|1|0:0
chr21	10559451	.	C	T	.	.	AN=4;AC=2	GT:PS	0|1|1|0:0	1|0|0|0:0
chr21	10560194	.	A	T	.	.	AN=4;AC=2	GT:PS	0|1|1|0:1	1|0|0|0:0
chr21	10560958	.	G	C	.	.	AN=4;AC=1	GT:PS	1|0|0|0:1	1|0|0|0:0
chr22	10561171	.	T	G	.	.	AN=4;AC=1	GT:PS	1|0|0|0:2	1|0|0|0:1
chr22	10561516	.	G	T	.	.	AN=4;AC=0	GT:PS	0|1|0|0:2	0|1|0|1:1
chr22	10561588	.	T	G	.	.	AN=4;AC=1	GT:PS	0|0|0|1:3	0|0|1|0:1
chr22	10561922	.	C	T	.	.	AN=4;AC=1	GT:PS	0/0/0/1:.	1|0|1|0:1
chr22	10562033	.	T	C	.	.	AN=4;AC=1	GT:PS	1|0|0|0:3	0|1|0|0:2
chr22	10562407	.	G	A	.	.	AN=4;AC=1	GT:PS	0|1|0|0:3	0|0|1|0:2
chr22	10564936	.	C	T	.	.	AN=4;AC=1	GT:PS	0|1|0|0:3	1|0|1|0:2
chr22	10565319	.	G	T	.	.	AN=4;AC=0	GT:PS	0|0|0|0:3	0/0/1/1:.
chr22	10566762	.	C	T	.	.	AN=4;AC=1	GT:PS	0|0|1|0:3	0/0/0/1:.
chr22	10566807	.	C	T	.	.	AN=4;AC=1	GT:PS	1|0|0|0:3	0/0/0/0:.
