diff test-data/fna_ref_b_testing/snps.filt.vcf @ 20:3bbfe41787af draft

planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fna_ref_b_testing/snps.filt.vcf	Fri Mar 08 20:46:56 2019 -0500
@@ -0,0 +1,28 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20190211
+##source=freeBayes v1.2.0-dirty
+##reference=reference/ref.fa
+##contig=<ID=reference,length=700>
+##phasing=none
+##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700"
+##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=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
+##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
+##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
+##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=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##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>=60.0 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Mon Feb 11 11:46:35 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=Mon Feb 11 11:46:35 2019
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	fna_ref_b_testing
+reference	4	.	A	T	63.8794	.	AB=0;AO=2;DP=2;QA=80;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:2:0:0:2:80:-7.59179,-0.60206,0