90722fe965a89529d622dc70225dea8cf3924e32
chmalee
  Tue Aug 4 16:53:00 2020 -0700
Stage genome in a bottle trio vcf track, refs #25873

diff --git src/hg/makeDb/giab/download.sh src/hg/makeDb/giab/download.sh
new file mode 100755
index 0000000..c14cb76
--- /dev/null
+++ src/hg/makeDb/giab/download.sh
@@ -0,0 +1,47 @@
+set -e
+# get the hg38 AshkenazimTrio VCFS
+mkdir -p {hg19,hg38}/{ChineseTrio,AshkenazimTrio}
+pushd hg38/AshkenazimTrio
+# son:
+wget ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/NISTv3.3.2/GRCh38/HG002_GRCh38_GIAB_highconf_CG-Illfb-IllsentieonHC-Ion-10XsentieonHC-SOLIDgatkHC_CHROM1-22_v.3.3.2_highconf_triophased.vcf.gz
+wget ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/NISTv3.3.2/GRCh38/HG002_GRCh38_GIAB_highconf_CG-Illfb-IllsentieonHC-Ion-10XsentieonHC-SOLIDgatkHC_CHROM1-22_v.3.3.2_highconf_triophased.vcf.gz.tbi
+# father:
+wget ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG003_NA24149_father/NISTv3.3.2/GRCh38/HG003_GRCh38_GIAB_highconf_CG-Illfb-IllsentieonHC-Ion-10XsentieonHC_CHROM1-22_v.3.3.2_highconf.vcf.gz
+wget ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG003_NA24149_father/NISTv3.3.2/GRCh38/HG003_GRCh38_GIAB_highconf_CG-Illfb-IllsentieonHC-Ion-10XsentieonHC_CHROM1-22_v.3.3.2_highconf.vcf.gz.tbi
+# mother:
+wget ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG004_NA24143_mother/NISTv3.3.2/GRCh38/HG004_GRCh38_GIAB_highconf_CG-Illfb-IllsentieonHC-Ion-10XsentieonHC_CHROM1-22_v.3.3.2_highconf.vcf.gz
+wget ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG004_NA24143_mother/NISTv3.3.2/GRCh38/HG004_GRCh38_GIAB_highconf_CG-Illfb-IllsentieonHC-Ion-10XsentieonHC_CHROM1-22_v.3.3.2_highconf.vcf.gz.tbi
+popd
+pushd hg19/AshkenazimTrio
+# son:
+wget ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/NISTv3.3.2/GRCh37/HG002_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-22_v.3.3.2_highconf_triophased.vcf.gz
+wget ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/NISTv3.3.2/GRCh37/HG002_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-22_v.3.3.2_highconf_triophased.vcf.gz.tbi
+# father:
+wget ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG003_NA24149_father/NISTv3.3.2/GRCh37/HG003_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X_CHROM1-22_v.3.3.2_highconf.vcf.gz
+wget ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG003_NA24149_father/NISTv3.3.2/GRCh37/HG003_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X_CHROM1-22_v.3.3.2_highconf.vcf.gz.tbi
+# mother:
+wget ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG004_NA24143_mother/NISTv3.3.2/GRCh37/HG004_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X_CHROM1-22_v.3.3.2_highconf.vcf.gz
+wget ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG004_NA24143_mother/NISTv3.3.2/GRCh37/HG004_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X_CHROM1-22_v.3.3.2_highconf.vcf.gz.tbi
+popd
+pushd hg38/ChineseTrio
+# son:
+wget ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/ChineseTrio/HG005_NA24631_son/NISTv3.3.2/GRCh38/HG005_GRCh38_GIAB_highconf_CG-Illfb-IllsentieonHC-Ion-10XsentieonHC-SOLIDgatkHC_CHROM1-22_v.3.3.2_highconf.vcf.gz
+wget ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/ChineseTrio/HG005_NA24631_son/NISTv3.3.2/GRCh38/HG005_GRCh38_GIAB_highconf_CG-Illfb-IllsentieonHC-Ion-10XsentieonHC-SOLIDgatkHC_CHROM1-22_v.3.3.2_highconf.vcf.gz.tbi
+# father:
+wget ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/ChineseTrio/HG006_NA24694_father/NISTv3.3.2/GRCh38/HG006_GIAB_GRCh38_highconf_CG-IllFB-IllSNT-10X_CHROM1-22_v.3.3.2_highconf.vcf.gz
+wget ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/ChineseTrio/HG006_NA24694_father/NISTv3.3.2/GRCh38/HG006_GIAB_GRCh38_highconf_CG-IllFB-IllSNT-10X_CHROM1-22_v.3.3.2_highconf.vcf.gz.tbi
+# mother:
+wget ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/ChineseTrio/HG007_NA24695_mother/NISTv3.3.2/GRCh38/HG007_GIAB_GRCh38_highconf_CG-IllFB-IllSNT-10X_CHROM1-22_v.3.3.2_highconf.vcf.gz
+wget ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/ChineseTrio/HG007_NA24695_mother/NISTv3.3.2/GRCh38/HG007_GIAB_GRCh38_highconf_CG-IllFB-IllSNT-10X_CHROM1-22_v.3.3.2_highconf.vcf.gz.tbi
+popd
+pushd hg19/ChineseTrio
+# son:
+wget ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/ChineseTrio/HG005_NA24631_son/NISTv3.3.2/GRCh37/HG005_GRCh37_highconf_CG-IllFB-IllGATKHC-Ion-SOLID_CHROM1-22_v.3.3.2_highconf.vcf.gz
+wget ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/ChineseTrio/HG005_NA24631_son/NISTv3.3.2/GRCh37/HG005_GRCh37_highconf_CG-IllFB-IllGATKHC-Ion-SOLID_CHROM1-22_v.3.3.2_highconf.vcf.gz.tbi
+# father:
+wget ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/ChineseTrio/HG006_NA24694_father/NISTv3.3.2/GRCh37/HG006_GIAB_GRCh37_highconf_CG-IllFB-IllSNT-10X_CHROM1-22_v.3.3.2_highconf.vcf.gz
+wget ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/ChineseTrio/HG006_NA24694_father/NISTv3.3.2/GRCh37/HG006_GIAB_GRCh37_highconf_CG-IllFB-IllSNT-10X_CHROM1-22_v.3.3.2_highconf.vcf.gz.tbi
+# mother:
+wget ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/ChineseTrio/HG007_NA24695_mother/NISTv3.3.2/GRCh37/HG007_GIAB_GRCh37_highconf_CG-IllFB-IllSNT-10X_CHROM1-22_v.3.3.2_highconf.vcf.gz
+wget ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/ChineseTrio/HG007_NA24695_mother/NISTv3.3.2/GRCh37/HG007_GIAB_GRCh37_highconf_CG-IllFB-IllSNT-10X_CHROM1-22_v.3.3.2_highconf.vcf.gz.tbi
+popd