incomplete download of pgx-main

2025-08-18 12:12:55 +02:00
parent fe48df8676
commit 75c821b975
984 changed files with 0 additions and 878657 deletions
--- a/pgx-main/resources/cyp2c8/res_b37/allele_def_var.vcf.gz
+++ b/pgx-main/resources/cyp2c8/res_b37/allele_def_var.vcf.gz
--- a/pgx-main/resources/cyp2c8/res_b37/allele_def_var.vcf.gz.tbi
+++ b/pgx-main/resources/cyp2c8/res_b37/allele_def_var.vcf.gz.tbi
--- a/pgx-main/resources/cyp2c8/res_b37/common_plus_core_var.vcf.gz
+++ b/pgx-main/resources/cyp2c8/res_b37/common_plus_core_var.vcf.gz
--- a/pgx-main/resources/cyp2c8/res_b37/common_plus_core_var.vcf.gz.tbi
+++ b/pgx-main/resources/cyp2c8/res_b37/common_plus_core_var.vcf.gz.tbi
--- a/pgx-main/resources/cyp2c8/res_b37/sv_test.vcf
+++ b/pgx-main/resources/cyp2c8/res_b37/sv_test.vcf
@@ -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=DEL;END=96829255;SVLEN=;SVSIZE=32727;NCLUSTERS=10;CIPOS=-11,11;CIEND=-8,8
--- a/pgx-main/resources/cyp2c8/res_b37/sv_test.vcf~
+++ b/pgx-main/resources/cyp2c8/res_b37/sv_test.vcf~
@@ -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=DEL;END=96612671;SVLEN=;SVSIZE=90209;NCLUSTERS=10;CIPOS=-11,11;CIEND=-8,8
--- a/pgx-main/resources/cyp2c8/res_b37/sv_test3.vcf
+++ b/pgx-main/resources/cyp2c8/res_b37/sv_test3.vcf
@@ -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
--- a/pgx-main/resources/cyp2c8/res_b37/sv_test3.vcf~
+++ b/pgx-main/resources/cyp2c8/res_b37/sv_test3.vcf~
@@ -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
--- a/pgx-main/resources/cyp2c8/res_b37/test3.bed
+++ b/pgx-main/resources/cyp2c8/res_b37/test3.bed
@@ -1,3 +0,0 @@
-10	96796529	96829255
-12	48235320	48298814
-7	55086678	55279262
--- a/pgx-main/resources/cyp2c8/res_b37/test3.bed~
+++ b/pgx-main/resources/cyp2c8/res_b37/test3.bed~
@@ -1,3 +0,0 @@
-10	96522463	96612671
-12	48235320	48298814
-7	55086678	55279262
--- a/pgx-main/resources/cyp2c8/res_hg19/allele_def_var.vcf.gz
+++ b/pgx-main/resources/cyp2c8/res_hg19/allele_def_var.vcf.gz
--- a/pgx-main/resources/cyp2c8/res_hg19/allele_def_var.vcf.gz.tbi
+++ b/pgx-main/resources/cyp2c8/res_hg19/allele_def_var.vcf.gz.tbi
--- a/pgx-main/resources/cyp2c8/res_hg19/common_plus_core_var.vcf.gz
+++ b/pgx-main/resources/cyp2c8/res_hg19/common_plus_core_var.vcf.gz
--- a/pgx-main/resources/cyp2c8/res_hg19/common_plus_core_var.vcf.gz.tbi
+++ b/pgx-main/resources/cyp2c8/res_hg19/common_plus_core_var.vcf.gz.tbi
--- a/pgx-main/resources/cyp2c8/res_hg19/sv_test.vcf.gz
+++ b/pgx-main/resources/cyp2c8/res_hg19/sv_test.vcf.gz
--- a/pgx-main/resources/cyp2c8/res_hg19/sv_test.vcf.gz.tbi
+++ b/pgx-main/resources/cyp2c8/res_hg19/sv_test.vcf.gz.tbi
--- a/pgx-main/resources/cyp2c8/res_hg19/sv_test3.vcf.gz
+++ b/pgx-main/resources/cyp2c8/res_hg19/sv_test3.vcf.gz
--- a/pgx-main/resources/cyp2c8/res_hg19/sv_test3.vcf.gz.tbi
+++ b/pgx-main/resources/cyp2c8/res_hg19/sv_test3.vcf.gz.tbi
--- a/pgx-main/resources/cyp2c8/res_hg19/test3.bed
+++ b/pgx-main/resources/cyp2c8/res_hg19/test3.bed
@@ -1,3 +0,0 @@
-chr10	96796529	96829255
-chr12	48235320	48298814
-chr7	55086678	55279262
--- a/pgx-main/resources/cyp2c8/res_hg38/allele_def_var.vcf.gz
+++ b/pgx-main/resources/cyp2c8/res_hg38/allele_def_var.vcf.gz
--- a/pgx-main/resources/cyp2c8/res_hg38/allele_def_var.vcf.gz.tbi
+++ b/pgx-main/resources/cyp2c8/res_hg38/allele_def_var.vcf.gz.tbi
--- a/pgx-main/resources/cyp2c8/res_hg38/common_plus_core_var.vcf.gz
+++ b/pgx-main/resources/cyp2c8/res_hg38/common_plus_core_var.vcf.gz
--- a/pgx-main/resources/cyp2c8/res_hg38/common_plus_core_var.vcf.gz.tbi
+++ b/pgx-main/resources/cyp2c8/res_hg38/common_plus_core_var.vcf.gz.tbi
--- a/pgx-main/resources/cyp2c8/res_hg38/sv_test.vcf.gz
+++ b/pgx-main/resources/cyp2c8/res_hg38/sv_test.vcf.gz
--- a/pgx-main/resources/cyp2c8/res_hg38/sv_test.vcf.gz.tbi
+++ b/pgx-main/resources/cyp2c8/res_hg38/sv_test.vcf.gz.tbi
--- a/pgx-main/resources/cyp2c8/res_hg38/sv_test3.vcf.gz
+++ b/pgx-main/resources/cyp2c8/res_hg38/sv_test3.vcf.gz
--- a/pgx-main/resources/cyp2c8/res_hg38/sv_test3.vcf.gz.tbi
+++ b/pgx-main/resources/cyp2c8/res_hg38/sv_test3.vcf.gz.tbi
--- a/pgx-main/resources/cyp2c8/res_hg38/test3.bed
+++ b/pgx-main/resources/cyp2c8/res_hg38/test3.bed
@@ -1,3 +0,0 @@
-chr10	95036772	95069497
-chr12	47841537	47905022
-chr7	55019017	55211628