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view test-data/discosnp/vcf_file_paired.vcf @ 4:a4d4b2564a2a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 0ed02865f048ad7471ea79509c0e23162bc29166"
author iuc
date Fri, 14 Aug 2020 20:54:58 +0000
parents dc31aacc886b
children
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##fileformat=VCFv4.1
##filedate=2020814XX
##source=VCF_creator
##SAMPLE=file://discoRes_k_31_c_auto_D_0_P_1_b_0_coherentBWA_MEM.sam
##REF=<ID=REF,Number=1,Type=String,Description="Allele of the path Disco aligned with the least mismatches">
##FILTER=<ID=MULTIPLE,Description="Mapping type : PASS or MULTIPLE or .">
##INFO=<ID=Ty,Number=1,Type=String,Description="SNP, INS, DEL or .">
##INFO=<ID=Rk,Number=1,Type=Float,Description="SNP rank">
##INFO=<ID=UL,Number=1,Type=Integer,Description="length of the unitig left">
##INFO=<ID=UR,Number=1,Type=Integer,Description="length of the unitig right">
##INFO=<ID=CL,Number=1,Type=Integer,Description="length of the contig left">
##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=.,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
read661_contig0_position139_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0	62	3	C	G	.	MULTIPLE	Ty=SNP;Rk=0;UL=86;UR=261;CL=.;CR=.;Genome=C;Sd=1;XA=read547_51,read624_39,read871_45,read688_36,read201_34,read45_68,read71_47,read728_35,read302_36,read492_42,read901_69,read237_35,read912_67,read120_38,read779_39,read161_45,read63_55,read872_67,read281_36,read900_43,read891_67,read943_45,read793_31,read300_58,read168_52,read315_58,read650_53,read918_70,read839_58,read215_68,read388_62,read479_63,read543_64,read418_35,read515_39,read661_62,read77_54,read241_35,read427_43,read268_67,read115_36,read915_50,read838_45,read382_44,read811_38,read438_35,read503_52,read472_46,read804_70,read510_30,read500_30,read759_70,read855_70,read171_70,read51_28,read464_70,read36_27,read579_70,read140_70,read720_26,read906_25,read454_24,read187_70,read75_24,read5_24,read729_24,read702_23,read433_23,read118_22,read377_22,read914_70,read691_21,read270_21,read112_70,read459_20,read240_20	GT:DP:PL:AD:HQ	0/1:258:1927,18,1727:124,134:0,0
read780_contig0_position26_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1	43	2	A	T	.	MULTIPLE	Ty=SNP;Rk=0;UL=86;UR=52;CL=.;CR=.;Genome=A;Sd=1;XA=read653_58,read292_70,read858_59,read808_53,read335_36,read233_53,read596_53,read132_33,read721_66,read378_67,read103_53,read928_33,read998_31,read484_51,read834_38,read387_38,read182_41,read111_60,read272_70,read325_59,read853_44,read480_37,read559_67,read244_32,read642_43,read780_43,read8_32,read170_49,read602_66,read973_58,read475_46,read347_69,read843_49,read612_65,read153_51,read78_30,read85_70,read420_30,read899_70,read805_70,read303_70,read104_27,read970_27,read328_70,read806_70,read202_70,read757_26,read521_26,read962_70,read696_23,read566_70,read321_70,read649_20,read253_20	GT:DP:PL:AD:HQ	0/1:160:1260,18,1020:74,86:0,0
read656_contig0_position454_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1	62	1	T	A	.	MULTIPLE	Ty=SNP;Rk=0;UL=472;UR=261;CL=.;CR=.;Genome=T;Sd=1;XA=read639_58,read567_37,read836_63,read727_33,read44_68,read625_48,read121_42,read298_56,read840_35,read62_69,read868_60,read38_56,read629_55,read896_35,read213_36,read897_67,read837_50,read994_50,read756_48,read113_59,read32_52,read129_38,read575_68,read957_34,read765_69,read94_41,read218_34,read297_51,read437_50,read256_48,read322_70,read716_52,read101_62,read254_50,read198_36,read12_44,read905_61,read760_67,read185_52,read761_66,read311_51,read357_43,read260_70	GT:DP:PL:AD:HQ	0/1:224:1628,17,1548:110,114:0,0