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CreateNewAnnotations.sh
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CreateNewAnnotations.sh
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# This script details how I went from the downloaded GRCh37 file, into GRCh38 files.
# The sub-files in this process are for either alternative coordinates with insertions (ins.shifted) or just reformatted
# This script is meant to run from:
cd /mnt/common/DATABASES/REFERENCES/GRCh37/GNOMADSV/V2.1/
# Step 1 - run python script to split out and reformat 2 sub files, shifted and reformatted
python CreateAltPositionGnomAD.py -I gnomad_v2.1_sv.sites.bed -O gnomad_v2.1_sv.sites.bed.altered
# This makes these files:
#-rwxrwx--- 1 prichmond domain users 12M Aug 25 14:03 gnomad_v2.1_sv.sites.bed.altered.ins.shifted.bed
#-rwxrwx--- 1 prichmond domain users 12M Aug 25 14:03 gnomad_v2.1_sv.sites.bed.altered.ins.shifted.chr.bed
#-rwxrwx--- 1 prichmond domain users 96 Aug 25 14:03 gnomad_v2.1_sv.sites.bed.altered.ins.shifted.chr.bed.header
#drwxrwx--- 2 prichmond domain users 1.2K Aug 25 14:03 .
#-rwxrwx--- 1 prichmond domain users 42M Aug 25 14:03 gnomad_v2.1_sv.sites.bed.altered.reformatted.bed
#-rwxrwx--- 1 prichmond domain users 43M Aug 25 14:03 gnomad_v2.1_sv.sites.bed.altered.reformatted.chr.bed
#-rwxrwx--- 1 prichmond domain users 36M Aug 25 14:03 gnomad_v2.1_sv.sites.bed.altered.reformatted.chr.bed.header
# Step 2 - liftOver
# FOr details on this go look at that script
sh /mnt/common/Precision/LiftOver/RunLiftOver.sh
# This made these files:
# In: /mnt/common/DATABASES/REFERENCES/GRCh38/GNOMADSV/V2.1/
# gnomad_v2.1_sv.sites.altered.ins.shifted.chr.hg38.bed
# gnomad_v2.1_sv.sites.altered.reformatted.chr.hg38.bed
# Step 3 - Re-header lifted-over files
cat /mnt/common/DATABASES/REFERENCES/GRCh37/GNOMADSV/V2.1/gnomad_v2.1_sv.sites.bed.altered.reformatted.chr.bed.header \
/mnt/common/DATABASES/REFERENCES/GRCh38/GNOMADSV/V2.1/gnomad_v2.1_sv.sites.altered.reformatted.chr.hg38.bed \
> /mnt/common/DATABASES/REFERENCES/GRCh38/GNOMADSV/V2.1/gnomad_v2.1_sv.sites.bed.altered.reformatted.chr.hg38.headered.bed
cat /mnt/common/DATABASES/REFERENCES/GRCh37/GNOMADSV/V2.1/gnomad_v2.1_sv.sites.bed.altered.ins.shifted.chr.bed.header \
/mnt/common/DATABASES/REFERENCES/GRCh38/GNOMADSV/V2.1/gnomad_v2.1_sv.sites.altered.ins.shifted.chr.hg38.bed \
> /mnt/common/DATABASES/REFERENCES/GRCh38/GNOMADSV/V2.1/gnomad_v2.1_sv.sites.bed.altered.ins.shifted.chr.hg38.headered.bed
# Step 4 trim the 'chr'
sed -e 's/^chr//g' /mnt/common/DATABASES/REFERENCES/GRCh38/GNOMADSV/V2.1/gnomad_v2.1_sv.sites.bed.altered.ins.shifted.chr.hg38.headered.bed \
> /mnt/common/DATABASES/REFERENCES/GRCh38/GNOMADSV/V2.1/gnomad_v2.1_sv.sites.bed.altered.ins.shifted.hg38.bed
sed -e 's/^chr//g' /mnt/common/DATABASES/REFERENCES/GRCh38/GNOMADSV/V2.1/gnomad_v2.1_sv.sites.bed.altered.reformatted.chr.hg38.headered.bed \
> /mnt/common/DATABASES/REFERENCES/GRCh38/GNOMADSV/V2.1/gnomad_v2.1_sv.sites.bed.altered.reformatted.hg38.bed
# Step 5 split into sub-files for AnnotSV
# Full Reformatted
# gnomAD_AF
cut -f1,2,3,9 /mnt/common/DATABASES/REFERENCES/GRCh38/GNOMADSV/V2.1/gnomad_v2.1_sv.sites.bed.altered.reformatted.hg38.bed > \
/mnt/common/DATABASES/REFERENCES/GRCh38/GNOMADSV/V2.1/UserGNOMADSV-AF.bed
# gnomAD_NHOMALT
cut -f1,2,3,10 /mnt/common/DATABASES/REFERENCES/GRCh38/GNOMADSV/V2.1/gnomad_v2.1_sv.sites.bed.altered.reformatted.hg38.bed > \
/mnt/common/DATABASES/REFERENCES/GRCh38/GNOMADSV/V2.1/UserGNOMADSV-NHOMALT.bed
# Shifted Insertions
# gnomAD_AF
cut -f1,2,3,9 /mnt/common/DATABASES/REFERENCES/GRCh38/GNOMADSV/V2.1/gnomad_v2.1_sv.sites.bed.altered.reformatted.hg38.bed > \
/mnt/common/DATABASES/REFERENCES/GRCh38/GNOMADSV/V2.1/UserGNOMADSV-AF-insertions.bed
# gnomAD_NHOMALT
cut -f1,2,3,10 /mnt/common/DATABASES/REFERENCES/GRCh38/GNOMADSV/V2.1/gnomad_v2.1_sv.sites.bed.altered.reformatted.hg38.bed > \
/mnt/common/DATABASES/REFERENCES/GRCh38/GNOMADSV/V2.1/UserGNOMADSV-NHOMALT-insertions.bed
# Step 6 copy over to AnnotSV
ANNOTSVDIR=/mnt/common/Precision/AnnotSV/share/AnnotSV/Annotations_Human/Users/GRCh38/
# FtIncludedInSV
# Full reformatted
cp /mnt/common/DATABASES/REFERENCES/GRCh38/GNOMADSV/V2.1/UserGNOMADSV-AF.bed \
$ANNOTSVDIR/FtIncludedInSV/UserGNOMADSV-AF.bed
cp /mnt/common/DATABASES/REFERENCES/GRCh38/GNOMADSV/V2.1/UserGNOMADSV-NHOMALT.bed \
$ANNOTSVDIR/FtIncludedInSV/UserGNOMADSV-NHOMALT.bed
# Shifted insertions
cp /mnt/common/DATABASES/REFERENCES/GRCh38/GNOMADSV/V2.1/UserGNOMADSV-AF-insertions.bed \
$ANNOTSVDIR/FtIncludedInSV/UserGNOMADSV-AF-insertions.bed
cp /mnt/common/DATABASES/REFERENCES/GRCh38/GNOMADSV/V2.1/UserGNOMADSV-NHOMALT-insertions.bed \
$ANNOTSVDIR/FtIncludedInSV/UserGNOMADSV-NHOMALT-insertions.bed
#SVincludedInFt
# Full reformatted
cp /mnt/common/DATABASES/REFERENCES/GRCh38/GNOMADSV/V2.1/UserGNOMADSV-AF.bed \
$ANNOTSVDIR/SVincludedInFt/UserGNOMADSV-AF.bed
cp /mnt/common/DATABASES/REFERENCES/GRCh38/GNOMADSV/V2.1/UserGNOMADSV-NHOMALT.bed \
$ANNOTSVDIR/SVincludedInFt/UserGNOMADSV-NHOMALT.bed
# Shifted insertions
cp /mnt/common/DATABASES/REFERENCES/GRCh38/GNOMADSV/V2.1/UserGNOMADSV-AF-insertions.bed \
$ANNOTSVDIR/SVincludedInFt/UserGNOMADSV-AF-insertions.bed
cp /mnt/common/DATABASES/REFERENCES/GRCh38/GNOMADSV/V2.1/UserGNOMADSV-NHOMALT-insertions.bed \
$ANNOTSVDIR/SVincludedInFt/UserGNOMADSV-NHOMALT-insertions.bed