Download Latest Version
db.tar.gz (105.2 MB)
Get an email when there's a new version of hg38 package
| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| varscan.config | 2026-01-30 | 35 Bytes | |
| exome_test38.sh | 2026-01-30 | 54.5 kB | |
| README | 2026-01-30 | 1.6 kB | |
| rna_test38.sh | 2026-01-02 | 51.2 kB | |
| cnvkit38.sh | 2025-02-11 | 10.4 kB | |
| somatic38.sh | 2024-12-10 | 17.7 kB | |
| itd_test38.sh | 2024-10-07 | 13.3 kB | |
| meerkat38.sh | 2024-10-07 | 17.3 kB | |
| config38.tmp | 2024-09-30 | 1.3 kB | |
| db.tar.gz | 2024-09-30 | 105.2 MB | |
| STAR | 2024-09-18 | 8.7 MB | |
| rmsk-hg38.txt | 2024-09-18 | 491.8 MB | |
| target38.bed | 2024-09-18 | 4.6 MB | |
| hg38.len | 2024-09-18 | 454 Bytes | |
| cnvkit.target38.bed | 2024-09-18 | 6.8 MB | |
| pon_hg38.cnn | 2024-09-18 | 14.5 MB | |
| cnv_annotate38.sh | 2024-09-18 | 562 Bytes | |
| refGene38_sorted.txt | 2024-09-18 | 25.7 MB | |
| svdetect_annotate38.sh | 2024-09-18 | 599 Bytes | |
| gene_cytoband38.txt | 2024-09-18 | 1.3 MB | |
| splitgtf.sh | 2024-09-18 | 306 Bytes | |
| dbsnpnew38.sh | 2024-09-18 | 2.9 kB | |
| createdict.sh | 2024-09-18 | 783 Bytes | |
| svdetect38.sh | 2024-09-18 | 52.6 kB | |
| svdetectcnv38.sh | 2024-09-18 | 14.8 kB | |
| Totals: 25 Items | 658.8 MB | 0 |
hg38 version of the pipelines for
whole exome sequencing: exome_test38.sh
wole transcription sequencing: rna_test38.sh
somatic calling: somatic38.sh
SV detect: svdetect38.sh, meerkat38.sh
cnv: svdetectcnv38.sh, contra38.sh, cnvkit38.sh
itd: itd_test38.sh
[INSTALLATION]
1. Install individual programs and references for hg38 according to the hg19 versions.
2. Download latest hg38 version of filters for ANNOVAR, including dbnsfp47a, clinvar_20240611, cosmic70 and avsnp151 to humandb38. Make Cosmic100 according to the ANNOVAR instruction. Remove ";" and "," from hg38_cosmic100.txt.
3. There seem problems with STAR 4.7 for variant calling. Use older version instead (provided here).
4. Download recent gatk (4.6 above) to /path/to/programs/gatk.
5. create directories of hg38_gtf, gene38_loc, cytoband38_loc and dbSNPnew38 (scripts provided here).
6. A PON file (pon_hg38.cnn) of normal reference is provided for cnvkit38. Run as
sh cnvkit38.sh tumor_name pon_hg38 cnv_folder
7. Create /path/to/programs/Genomon-ITDetector-master-hg38/ref38 for itd_test38.sh. Create 11.ooc and out.2bit usging hg38.fa. The hg38 version of config38.tmp and db files can be downloaded here.
./faToTwoBit hg38.fa out.2bit
./blat -makeOoc=11.ooc -repMatch=2253 -tileSize=11 out.2bit temp.fa temp.psl
8. Create target38.intervals folder using following script:
awk -F '\t' '{print $0 >> "/path/to/software/target38_intervals/" $1 ".bed"}' /path/to/target38.bed (provided here)
9. Write the Varscan options to /path/to/software/varscan.config.
