diff test-data/discosnp/vcf_file.vcf @ 4:435a98f01ae9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 0ed02865f048ad7471ea79509c0e23162bc29166"
author iuc
date Mon, 17 Aug 2020 10:38:08 -0400
parents 13c8e1ce0a15
children
line wrap: on
line diff
--- a/test-data/discosnp/vcf_file.vcf	Wed Jan 22 17:27:07 2020 -0500
+++ b/test-data/discosnp/vcf_file.vcf	Mon Aug 17 10:38:08 2020 -0400
@@ -1,5 +1,5 @@
 ##fileformat=VCFv4.1
-##filedate=2017102
+##filedate=2020814XX
 ##source=VCF_creator
 ##SAMPLE=file://discoRes_k_25_c_auto_D_0_P_1_b_0_coherent.fa
 ##REF=<ID=REF,Number=1,Type=String,Description="Allele of the path Disco aligned with the least mismatches">
@@ -12,13 +12,13 @@
 ##INFO=<ID=CR,Number=1,Type=Integer,Description="length of the contig right">
 ##INFO=<ID=Genome,Number=1,Type=String,Description="Allele of the reference;for indel reference is . ">
 ##INFO=<ID=Sd,Number=1,Type=Integer,Description="Reverse (-1) or Forward (1) Alignement">
-##INFO=<ID=XA,Number=0/1,Type=String,Description="Other mapping positions (chromosome_position). Position is negative in case of Reverse alignment. The position designs the starting position of the alignment, not the position of the variant itself.">
+##INFO=<ID=XA,Number=.,Type=String,Description="Other mapping positions (chromosome_position). Position is negative in case of Reverse alignment. The position designs the starting position of the alignment, not the position of the variant itself.">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Cumulated depth accross samples (sum)">
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled Genotype Likelihoods">
 ##FORMAT=<ID=AD,Number=2,Type=Integer,Description="Depth of each allele by sample">
 ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	G1	G2
-SNP_higher_path_3	24	3	A	T	.	.	Ty=SNP;Rk=1;UL=.;UR=.;CL=.;CR=.;Genome=.;Sd=.	GT:DP:PL:AD:HQ	0/0:74:8,227,1484:74,0:0,0	1/1:86:1724,263,8:0,86:0,0
-SNP_higher_path_2	24	2	C	G	.	.	Ty=SNP;Rk=1;UL=.;UR=.;CL=.;CR=.;Genome=.;Sd=.	GT:DP:PL:AD:HQ	1/1:124:2484,378,10:0,124:0,0	0/0:134:10,408,2684:134,0:0,0
-SNP_higher_path_1	24	1	A	T	.	.	Ty=SNP;Rk=1;UL=.;UR=.;CL=.;CR=.;Genome=.;Sd=.	GT:DP:PL:AD:HQ	1/1:110:2204,335,9:0,110:0,0	0/0:114:9,347,2284:114,0:0,0
+SNP_higher_path_3	116	3	A	T	.	.	Ty=SNP;Rk=1;UL=92;UR=55;CL=.;CR=.;Genome=.;Sd=.	GT:DP:PL:AD:HQ	0/0:74:8,227,1484:74,0:0,0	1/1:86:1724,263,8:0,86:0,0
+SNP_higher_path_2	291	2	C	G	.	.	Ty=SNP;Rk=1;UL=267;UR=92;CL=.;CR=.;Genome=.;Sd=.	GT:DP:PL:AD:HQ	1/1:124:2484,378,10:0,124:0,0	0/0:134:10,408,2684:134,0:0,0
+SNP_higher_path_1	499	1	A	T	.	.	Ty=SNP;Rk=1;UL=475;UR=267;CL=.;CR=.;Genome=.;Sd=.	GT:DP:PL:AD:HQ	1/1:110:2204,335,9:0,110:0,0	0/0:114:9,347,2284:114,0:0,0