|
grch37-reference-genome
|
public |
No Summary
|
2025-03-25 |
|
hg19-phastcons
|
public |
phastCons scores for MSA of 99 genomes to hg19
|
2025-03-25 |
|
hg19-gaps
|
public |
Assembly gaps from UCSC
|
2025-03-25 |
|
hg19-simplerepeats
|
public |
Simple reoeats track from UCSC.
name=sequence score=alignment score
col 7 = period
col 8 = copy_num
|
2025-03-25 |
|
hg19-repeatmasker
|
public |
RepeatMasker track from UCSC. name=family_class_name score=milliDic+milliDel+milliIns
|
2025-03-25 |
|
hg38-repeatmasker
|
public |
RepeatMasker track from UCSC. name=family_class_name score=milliDic+milliDel+milliIns
|
2025-03-25 |
|
grch37-radar
|
public |
RADAR RNA editing events: (http://www.stanford.edu/~gokulr/database/Human_AG_all_hg19_v2.txt)
installs a BED file of the RADAR events, converted to GRCh37 chromosome coordinates
|
2025-03-25 |
|
grch37-sequence
|
public |
fasta sequence from 1kg
|
2025-03-25 |
|
hg19-radar
|
public |
RADAR RNA editing events: (http://www.stanford.edu/~gokulr/database/Human_AG_all_hg19_v2.txt)
installs a BED file of the RADAR events
|
2025-03-25 |
|
hg38-noalt-sequence
|
public |
Reference genome distributed by NCBI for GRCh38, without alternative reference contigs
|
2025-03-25 |
|
hg38-sequence
|
public |
Full hg38/GRCh38 reference genome distributed by 1000 genomes
Derived from NCBI set with HLA and decoy alternative alleles
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/
|
2025-03-25 |
|
hg38-reference
|
public |
No Summary
|
2025-03-25 |
|
mm10-transcripts
|
public |
Transcript, annotation and indices for RNA-seq analysis
Prepared from Ensembl transcripts using:
https://github.com/chapmanb/cloudbiolinux/blob/master/utils/prepare_tx_gff.py
|
2025-03-25 |
|
mm10-srnaseq
|
public |
small RNA seq annotation from different sources
|
2025-03-25 |
|
mm10-problem_regions
|
public |
Problematic genomic regions for annotations and improving variant call comparisons
mm10 LCRs from Brent Pedersen: http://figshare.com/articles/LCR_mm10_bed_gz/1180124
|
2025-03-25 |
|
mm10-dbsnp
|
public |
No Summary
|
2025-03-25 |
|
hg38-transcripts
|
public |
Transcript, annotation and indices for RNA-seq analysis
Prepared from Ensembl transcripts using:
https://github.com/chapmanb/cloudbiolinux/blob/master/utils/prepare_tx_gff.py
|
2025-03-25 |
|
hg38-seq
|
public |
Full hg38/GRCh38 reference genome distributed by 1000 genomes
Derived from NCBI set with HLA and decoy alternative alleles
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/
|
2025-03-25 |
|
hg38-radar-hg38
|
public |
RADAR RNA editing events: (http://www.stanford.edu/~gokulr/database/Human_AG_all_hg19_v2.txt)
installs a BED file of the RADAR events, preconverted to hg38
how this file was created:
1. Download the hg19 RADAR file and converted to BED format.
url=http://www.stanford.edu/~gokulr/database/Human_AG_all_hg19_v2.txt
mkdir -p editing
cd editing
wget -qO- $url | awk 'BEGIN{OFS="\t"} {print $1,$2,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11}' | sed "s/position position/start end/" > RADAR-hg19.bed
cd ../
2. Convert RADAR BED file to BED3 format.
cut -f1,2,3 RADAR-hg19.bed > RADAR-hg19.tmp.bed
3. Get the Crossmap hg19 to hg38 chain file:
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz
4. Run Crossmap:
Crossmap.py bed hg19ToHg38.over.chain.gz RADAR-hg19.tmp.bed > conversions.bed
5. Merge original RADAR file with the Crossmap output
wget https://raw.githubusercontent.com/roryk/seqscripts/master/radar-convert-annotations.py
python radar-convert-annotations.py RADAR-hg19.bed conversions.bed RADAR-hg38.bed.gz
|
2025-03-25 |
|
hg38-prioritize
|
public |
Regions for prioritization:
cancer
- civic -- known cancer genes from the CIViC database
- az300 -- list of 300 cancer genes of interest from AstraZeneca Oncology
- az300-with-fusion -- az300 list plus known interacting fusions
from FusionCatcher https://github.com/ndaniel/fusioncatcher/blob/master/bin/generate_known.py#L102
- az-cancer-panel -- az300 genes plus additional useful panel genes
|
2025-03-25 |
|
hg38-platinum-genome-na12878
|
public |
Truth sets from Illumina Platinum Genomes project
http://www.illumina.com/platinumgenomes/
|
2025-03-25 |
|
hg38-noalt-transcripts
|
public |
Transcript, annotation and indices for RNA-seq analysis
Prepared from Ensembl transcripts using:
https://github.com/chapmanb/cloudbiolinux/blob/master/utils/prepare_tx_gff.py
|
2025-03-25 |
|
hg38-noalt-seq
|
public |
Reference genome distributed by NCBI for GRCh38, without alternative reference contigs
|
2025-03-25 |
|
hg38-noalt-radar-hg38
|
public |
RADAR RNA editing events: (http://www.stanford.edu/~gokulr/database/Human_AG_all_hg19_v2.txt)
installs a BED file of the RADAR events, preconverted to hg38
how this file was created:
1. Download the hg19 RADAR file and converted to BED format.
url=http://www.stanford.edu/~gokulr/database/Human_AG_all_hg19_v2.txt
mkdir -p editing
cd editing
wget -qO- $url | awk 'BEGIN{OFS="\t"} {print $1,$2,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11}' | sed "s/position position/start end/" > RADAR-hg19.bed
cd ../
2. Convert RADAR BED file to BED3 format.
cut -f1,2,3 RADAR-hg19.bed > RADAR-hg19.tmp.bed
3. Get the Crossmap hg19 to hg38 chain file:
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz
4. Run Crossmap:
Crossmap.py bed hg19ToHg38.over.chain.gz RADAR-hg19.tmp.bed > conversions.bed
5. Merge original RADAR file with the Crossmap output
wget https://raw.githubusercontent.com/roryk/seqscripts/master/radar-convert-annotations.py
python radar-convert-annotations.py RADAR-hg19.bed conversions.bed RADAR-hg38.bed.gz
|
2025-03-25 |
|
hg38-noalt-mills_indels
|
public |
Curated training indels from Mills et al:
http://genome.cshlp.org/content/21/6/830.full
From the Broad v2.8 resource bundle
https://www.broadinstitute.org/gatk/guide/article.php?id=1213
lifted over to hg38 coordinates by Alison Meynert
https://github.com/chapmanb/bcbio-nextgen/issues/817
|
2025-03-25 |
