##fileformat=VCFv4.2
##snippy="snippy-vcf_extract_subs snps.filt.vcf"
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20190118
##source=freeBayes v1.2.0-dirty
##reference=reference/ref.fa
##contig=<ID=Wildtype,length=197394>
##phasing=none
##commandline="freebayes -p 2 -P 0 -C 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 10 -F 0.05 -f reference/ref.fa snps.bam --region Wildtype:0-13379"
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
##bcftools_viewVersion=1.9+htslib-1.9
##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf; Date=Fri Jan 18 16:21:02 2019
##bcftools_annotateVersion=1.9+htslib-1.9
##bcftools_annotateCommand=annotate --remove ^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL; Date=Fri Jan 18 16:21:02 2019
##INFO=<ID=OLDVAR,Number=R,Type=String,Description="Original REF,ALT before decomposition">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	out
Wildtype	24388	.	A	G	673.635	.	TYPE=snp;DP=22;RO=0;AO=22	GT:DP:RO:AO:QR:QA	1/1:22:0:22:0:785
Wildtype	29479	.	T	G	673.562	.	TYPE=snp;DP=21;RO=0;AO=21	GT:DP:RO:AO:QR:QA	1/1:21:0:21:0:776
Wildtype	47299	.	T	A	772.746	.	TYPE=snp;DP=25;RO=0;AO=25	GT:DP:RO:AO:QR:QA	1/1:25:0:25:0:921
Wildtype	102969	.	G	C	548.461	.	TYPE=snp;DP=18;RO=0;AO=18	GT:DP:RO:AO:QR:QA	1/1:18:0:18:0:637
Wildtype	103048	.	T	A	659.012	.	TYPE=snp;DP=23;RO=0;AO=23	GT:DP:RO:AO:QR:QA	1/1:23:0:23:0:766
Wildtype	106602	.	T	G	679.76	.	TYPE=snp;DP=22;RO=0;AO=22	GT:DP:RO:AO:QR:QA	1/1:22:0:22:0:790
Wildtype	109833	.	T	A	523.219	.	TYPE=snp;DP=17;RO=0;AO=17	GT:DP:RO:AO:QR:QA	1/1:17:0:17:0:612
Wildtype	129881	.	G	A	591.829	.	TYPE=snp;DP=19;RO=0;AO=19;OLDVAR=mnp,129881,GT,AA	GT:DP:RO:AO:QR:QA	1/1:19:0:19:0:686
Wildtype	129882	.	T	A	591.829	.	TYPE=snp;DP=19;RO=0;AO=19;OLDVAR=mnp,129881,GT,AA	GT:DP:RO:AO:QR:QA	1/1:19:0:19:0:686
Wildtype	138877	.	G	C	433.927	.	TYPE=snp;DP=14;RO=0;AO=14	GT:DP:RO:AO:QR:QA	1/1:14:0:14:0:507
Wildtype	138954	.	A	G	302.917	.	TYPE=snp;DP=10;RO=0;AO=10	GT:DP:RO:AO:QR:QA	1/1:10:0:10:0:354