# 2026-05-18 Claude max

# SweGen 1000 Swedish WGS, recomputed against T2T-CHM13.
# File received from SweFreq/SciLifeLab via the public SweGen download form at
#   https://swefreq.nbis.se/dataset/SweGen
# Used as-is, no further processing.

cd /hive/data/genomes/hs1/bed/varFreqs/swegen
# SweGen_T2T-CHM13_RefSeq_20251201.vcf.gz was placed here; tabix .tbi was
# copied from the parallel hg38 directory where the same file had been
# downloaded earlier (identical md5).

# Symlink into /gbdb under the same dir name (_swefreq) and filename used by
# the shared hg38 swefreq trackDb stanza so the parent's bigDataUrl
# (/gbdb/$D/varFreqs/_swefreq/swegen_frequencies_fixploidy_GRCh38_20190204.vcf.gz)
# resolves correctly on hs1 with no override needed.
mkdir -p /gbdb/hs1/varFreqs/_swefreq
cd /gbdb/hs1/varFreqs/_swefreq
ln -s /hive/data/genomes/hs1/bed/varFreqs/swegen/SweGen_T2T-CHM13_RefSeq_20251201.vcf.gz \
      swegen_frequencies_fixploidy_GRCh38_20190204.vcf.gz
ln -s /hive/data/genomes/hs1/bed/varFreqs/swegen/SweGen_T2T-CHM13_RefSeq_20251201.vcf.gz.tbi \
      swegen_frequencies_fixploidy_GRCh38_20190204.vcf.gz.tbi
