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incomplete download of pgx-main

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Darren Wight
2025-08-18 12:12:55 +02:00
parent fe48df8676
commit 75c821b975
984 changed files with 0 additions and 878657 deletions
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pgx-main/resources/cyp2c8/res_b37/allele_def_var.vcf.gz
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pgx-main/resources/cyp2c8/res_b37/allele_def_var.vcf.gz.tbi
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pgx-main/resources/cyp2c8/res_b37/common_plus_core_var.vcf.gz
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pgx-main/resources/cyp2c8/res_b37/sv_test.vcf
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##fileformat=VCFv4.2
##contig=<ID=10,length=135534747>
##fileDate=20200316
##reference=reference.fa
##phasing=true
##INFO=<ID=COMPACT_TP,Number=.,Type=String,Description="">
##INFO=<ID=SEQ,Number=1,Type=String,Description="Sequence to insert.">
##INFO=<ID=TYPE,Number=A,Type=String,Description="Type of each allele (snp, ins, del, mnp, complex)">
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=SVSIZE,Number=.,Type=Integer,Description="Absolute value of SVLEN">
##INFO=<ID=NCLUSTERS,Number=1,Type=Integer,Description="Number of clipped read clusters used for prediction">
##INFO=<ID=NUM_MERGED_SVS,Number=1,Type=Integer,Description="Number of merged SVs.">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical homology at event breakpoints">
##INFO=<ID=SVINSSEQ,Number=.,Type=String,Description="Sequence of insertion">
##INFO=<ID=LEFT_SVINSSEQ,Number=.,Type=String,Description="Known left side of insertion for an insertion of unknown length">
##INFO=<ID=RIGHT_SVINSSEQ,Number=.,Type=String,Description="Known right side of insertion for an insertion of unknown length">
##INFO=<ID=INV3,Number=0,Type=Flag,Description="Inversion breakends open 3' of reported location">
##INFO=<ID=INV5,Number=0,Type=Flag,Description="Inversion breakends open 5' of reported location">
#CHROM POS ID REF ALT QUAL FILTER INFO
10 96796529 . T <DEL> 99 . IMPRECISE;SVTYPE=DEL;END=96829255;SVLEN=;SVSIZE=32727;NCLUSTERS=10;CIPOS=-11,11;CIEND=-8,8

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pgx-main/resources/cyp2c8/res_b37/sv_test.vcf~
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##fileformat=VCFv4.2
##contig=<ID=10,length=135534747>
##fileDate=20200316
##reference=reference.fa
##phasing=true
##INFO=<ID=COMPACT_TP,Number=.,Type=String,Description="">
##INFO=<ID=SEQ,Number=1,Type=String,Description="Sequence to insert.">
##INFO=<ID=TYPE,Number=A,Type=String,Description="Type of each allele (snp, ins, del, mnp, complex)">
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=SVSIZE,Number=.,Type=Integer,Description="Absolute value of SVLEN">
##INFO=<ID=NCLUSTERS,Number=1,Type=Integer,Description="Number of clipped read clusters used for prediction">
##INFO=<ID=NUM_MERGED_SVS,Number=1,Type=Integer,Description="Number of merged SVs.">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical homology at event breakpoints">
##INFO=<ID=SVINSSEQ,Number=.,Type=String,Description="Sequence of insertion">
##INFO=<ID=LEFT_SVINSSEQ,Number=.,Type=String,Description="Known left side of insertion for an insertion of unknown length">
##INFO=<ID=RIGHT_SVINSSEQ,Number=.,Type=String,Description="Known right side of insertion for an insertion of unknown length">
##INFO=<ID=INV3,Number=0,Type=Flag,Description="Inversion breakends open 3' of reported location">
##INFO=<ID=INV5,Number=0,Type=Flag,Description="Inversion breakends open 5' of reported location">
#CHROM POS ID REF ALT QUAL FILTER INFO
10 96522463 . A <DEL> 99 . IMPRECISE;SVTYPE=DEL;END=96612671;SVLEN=;SVSIZE=90209;NCLUSTERS=10;CIPOS=-11,11;CIEND=-8,8

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pgx-main/resources/cyp2c8/res_b37/sv_test3.vcf
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@@ -1,25 +0,0 @@
##fileformat=VCFv4.2
##contig=<ID=10,length=135534747>
##fileDate=20200316
##reference=reference.fa
##phasing=true
##INFO=<ID=COMPACT_TP,Number=.,Type=String,Description="">
##INFO=<ID=SEQ,Number=1,Type=String,Description="Sequence to insert.">
##INFO=<ID=TYPE,Number=A,Type=String,Description="Type of each allele (snp, ins, del, mnp, complex)">
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=SVSIZE,Number=.,Type=Integer,Description="Absolute value of SVLEN">
##INFO=<ID=NCLUSTERS,Number=1,Type=Integer,Description="Number of clipped read clusters used for prediction">
##INFO=<ID=NUM_MERGED_SVS,Number=1,Type=Integer,Description="Number of merged SVs.">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical homology at event breakpoints">
##INFO=<ID=SVINSSEQ,Number=.,Type=String,Description="Sequence of insertion">
##INFO=<ID=LEFT_SVINSSEQ,Number=.,Type=String,Description="Known left side of insertion for an insertion of unknown length">
##INFO=<ID=RIGHT_SVINSSEQ,Number=.,Type=String,Description="Known right side of insertion for an insertion of unknown length">
##INFO=<ID=INV3,Number=0,Type=Flag,Description="Inversion breakends open 3' of reported location">
##INFO=<ID=INV5,Number=0,Type=Flag,Description="Inversion breakends open 5' of reported location">
#CHROM POS ID REF ALT QUAL FILTER INFO
10 96796529 . T <DEL> 99 . IMPRECISE;SVTYPE=DUP;SVLEN=+32727;SVSIZE=32727

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pgx-main/resources/cyp2c8/res_b37/sv_test3.vcf~
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@@ -1,25 +0,0 @@
##fileformat=VCFv4.2
##contig=<ID=10,length=135534747>
##fileDate=20200316
##reference=reference.fa
##phasing=true
##INFO=<ID=COMPACT_TP,Number=.,Type=String,Description="">
##INFO=<ID=SEQ,Number=1,Type=String,Description="Sequence to insert.">
##INFO=<ID=TYPE,Number=A,Type=String,Description="Type of each allele (snp, ins, del, mnp, complex)">
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=SVSIZE,Number=.,Type=Integer,Description="Absolute value of SVLEN">
##INFO=<ID=NCLUSTERS,Number=1,Type=Integer,Description="Number of clipped read clusters used for prediction">
##INFO=<ID=NUM_MERGED_SVS,Number=1,Type=Integer,Description="Number of merged SVs.">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical homology at event breakpoints">
##INFO=<ID=SVINSSEQ,Number=.,Type=String,Description="Sequence of insertion">
##INFO=<ID=LEFT_SVINSSEQ,Number=.,Type=String,Description="Known left side of insertion for an insertion of unknown length">
##INFO=<ID=RIGHT_SVINSSEQ,Number=.,Type=String,Description="Known right side of insertion for an insertion of unknown length">
##INFO=<ID=INV3,Number=0,Type=Flag,Description="Inversion breakends open 3' of reported location">
##INFO=<ID=INV5,Number=0,Type=Flag,Description="Inversion breakends open 5' of reported location">
#CHROM POS ID REF ALT QUAL FILTER INFO
10 96522463 . A <DEL> 99 . IMPRECISE;SVTYPE=DUP;SVLEN=+90209;SVSIZE=90209

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pgx-main/resources/cyp2c8/res_b37/test3.bed
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@@ -1,3 +0,0 @@
10 96796529 96829255
12 48235320 48298814
7 55086678 55279262

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pgx-main/resources/cyp2c8/res_b37/test3.bed~
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@@ -1,3 +0,0 @@
10 96522463 96612671
12 48235320 48298814
7 55086678 55279262