diff test-data/rif_resistant.vcf @ 0:02d81b994ef5 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
author iuc
date Thu, 29 Aug 2019 08:18:59 -0400
parents
children 42818629ec4c
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rif_resistant.vcf	Thu Aug 29 08:18:59 2019 -0400
@@ -0,0 +1,53 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##bcftoolsVersion=1.9+htslib-1.9
+##bcftoolsCommand=mpileup --fasta-ref /home/pvh/Data/fasta/Mycobacterium_tuberculosis_h37rv.GCA_000195955.2.29.dna.chromosome.Chromosome.fa rif_resistant.bam
+##reference=file:///home/pvh/Data/fasta/Mycobacterium_tuberculosis_h37rv.GCA_000195955.2.29.dna.chromosome.Chromosome.fa
+##contig=<ID=MT_H37RV_BRD_V5,length=4411532>
+##ALT=<ID=*,Description="Represents allele(s) other than observed.">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
+##INFO=<ID=AF2,Number=1,Type=Float,Description="Max-likelihood estimate of the first and second group ALT allele frequency (assuming HWE)">
+##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
+##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
+##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
+##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
+##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
+##bcftools_callVersion=1.9+htslib-1.9
+##bcftools_callCommand=call --ploidy 1 -c -v rif_resistant.mpileup; Date=Tue Apr  2 06:47:33 2019
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	rif_resistant.bam
+MT_H37RV_BRD_V5	15890	.	G	A	225.007	.	DP=58;VDB=0.0163018;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,29,24;MQ=60;FQ=-999	GT:PL	1:255,0
+MT_H37RV_BRD_V5	154990	.	G	T	225.007	.	DP=57;VDB=0.997362;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,18,38;MQ=60;FQ=-999	GT:PL	1:255,0
+MT_H37RV_BRD_V5	346693	.	G	T	225.007	.	DP=27;VDB=0.365109;SGB=-0.692976;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,14,12;MQ=60;FQ=-999	GT:PL	1:255,0
+MT_H37RV_BRD_V5	449194	.	G	A	225.007	.	DP=29;VDB=0.387982;SGB=-0.692976;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,5,21;MQ=60;FQ=-999	GT:PL	1:255,0
+MT_H37RV_BRD_V5	497491	.	G	A	225.007	.	DP=78;VDB=0.57291;SGB=-0.693147;MQSB=0.99133;MQ0F=0;AF1=1;AC1=1;DP4=0,0,53,24;MQ=60;FQ=-999	GT:PL	1:255,0
+MT_H37RV_BRD_V5	761110	.	A	T	225.007	.	DP=59;VDB=0.35459;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,25,32;MQ=60;FQ=-999	GT:PL	1:255,0
+MT_H37RV_BRD_V5	763031	.	T	C	225.007	.	DP=85;VDB=0.401561;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,38,46;MQ=60;FQ=-999	GT:PL	1:255,0
+MT_H37RV_BRD_V5	811753	.	C	T	225.007	.	DP=55;VDB=0.241716;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,27,24;MQ=60;FQ=-999	GT:PL	1:255,0
+MT_H37RV_BRD_V5	1565566	.	C	T	225.007	.	DP=52;VDB=0.650985;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,13,36;MQ=60;FQ=-999	GT:PL	1:255,0
+MT_H37RV_BRD_V5	1833729	.	TCCCC	TCCCCCC	12.7055	.	INDEL;IDV=1;IMF=1;DP=1;SGB=-0.379885;MQ0F=0;AF1=1;AC1=1;DP4=0,0,0,1;MQ=54;FQ=-999	GT:PL	1:50,3,0
+MT_H37RV_BRD_V5	1834177	.	A	C	225.007	.	DP=76;VDB=0.880419;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,42,29;MQ=60;FQ=-999	GT:PL	1:255,0
+MT_H37RV_BRD_V5	1849051	.	C	T	225.007	.	DP=86;VDB=0.199205;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,38,45;MQ=60;FQ=-999	GT:PL	1:255,0
+MT_H37RV_BRD_V5	2505085	.	G	A	225.007	.	DP=48;VDB=0.280048;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,32,13;MQ=60;FQ=-999	GT:PL	1:255,0
+MT_H37RV_BRD_V5	2543395	.	T	C	225.007	.	DP=88;VDB=0.167176;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,37,46;MQ=60;FQ=-999	GT:PL	1:255,0
+MT_H37RV_BRD_V5	2640807	.	G	A	225.007	.	DP=55;VDB=0.218547;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,29,21;MQ=60;FQ=-999	GT:PL	1:255,0
+MT_H37RV_BRD_V5	2775361	.	C	T	225.007	.	DP=99;VDB=0.0864314;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,46,44;MQ=60;FQ=-999	GT:PL	1:255,0
+MT_H37RV_BRD_V5	2789798	.	G	T	225.007	.	DP=72;VDB=0.231858;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,33,35;MQ=60;FQ=-999	GT:PL	1:255,0
+MT_H37RV_BRD_V5	3477942	.	A	G	225.007	.	DP=100;VDB=0.912557;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,45,52;MQ=60;FQ=-999	GT:PL	1:255,0
+MT_H37RV_BRD_V5	3587446	.	G	A	225.007	.	DP=59;VDB=0.0078857;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,33,24;MQ=60;FQ=-999	GT:PL	1:255,0
+MT_H37RV_BRD_V5	4254431	.	G	A	225.007	.	DP=58;VDB=0.120561;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,25,33;MQ=60;FQ=-999	GT:PL	1:255,0
+MT_H37RV_BRD_V5	4254477	.	T	C	225.007	.	DP=30;VDB=0.000342098;SGB=-0.693021;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,10,17;MQ=60;FQ=-999	GT:PL	1:255,0