ggd-alpha
by ggd-alpha (Organization)
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| Name | Latest Version | Summary | Updated | License |
|---|
| hg38-clinvar | 20150330.2 | ClinVar: http://www.clinvar.com/ UCSFify name sed magic from: https://github.com/mmarchin/utilities/blob/master/ucscify.sh | Mar 25, 2025 | — |
| grch37-ga4gh-problem-regions | 20151116 | GA4GH problematic region files: https://drive.google.com/folderview?id=0B7Ao1qqJJDHQUjVIN3liUUZNWjg&usp=sharing#list | Mar 25, 2025 | — |
| grch37-qsignature | 20140703 | — | Mar 25, 2025 | — |
| hg19-cosmic | 68 | — | Mar 25, 2025 | — |
| mm10-dbsnp | 20130912 | — | Mar 25, 2025 | — |
| grch37-cosmic | 68 | — | Mar 25, 2025 | — |
| canfam3-dbsnp | 20140510 | — | Mar 25, 2025 | — |
| hg38-1000g_snps | 2.8_hg38_20150522 | 1000 genomes phase 1 SNP calls 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 | Mar 25, 2025 | — |
| hg38-radar-hg38 | 1 | 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 | Mar 25, 2025 | — |
| hg19-ancestral | 20141010 | — | Mar 25, 2025 | — |
| hg19-platinum-genome-na12878 | v8_0_1 | Truth sets from Illumina Platinum Genomes project http://www.illumina.com/platinumgenomes/ | Mar 25, 2025 | — |
| hg19-mig | 20150730 | Medically Interpretable Genes, compiled by Personalis: http://www.genomemedicine.com/content/pdf/s13073-015-0197-4.pdf | Mar 25, 2025 | — |
| hg19-srnaseq | 20160224 | small RNA seq annotation from different sources | Mar 25, 2025 | — |
| grch37-prioritize | 20160215 | 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 | Mar 25, 2025 | — |
| hg19-qsignature | 20140703 | — | Mar 25, 2025 | — |
| grch37-ancestral | 20141010 | — | Mar 25, 2025 | — |
| canfam3-transcripts | 2014.07.20 | 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 | Mar 25, 2025 | — |
| grch37-mig | 20150730 | Medically Interpretable Genes, compiled by Personalis: http://www.genomemedicine.com/content/pdf/s13073-015-0197-4.pdf | Mar 25, 2025 | — |
| hg38-gtf | 78 | Ensembl GTF file distributed by Ensembl for hg38 Cleans GTF file by converting chromosome names to standard names Uses https://github.com/dpryan79/ChromosomeMappings to remap the chromosome names | Mar 25, 2025 | — |
| hg38-platinum-genome-na12878 | v2_0_1 | Truth sets from Illumina Platinum Genomes project http://www.illumina.com/platinumgenomes/ | Mar 25, 2025 | — |
| grch37-1000g_omni_snps | 2.5 | — | Mar 25, 2025 | — |
| hg19-prioritize | 20160215 | 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 | Mar 25, 2025 | — |
| grch37-transcripts | 2015.12.01 | 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 | Mar 25, 2025 | — |
| hg19-dbnsfp | 3.1c | — | Mar 25, 2025 | — |
| hg19-ga4gh-problem-regions | 20151116 | GA4GH problematic region files: https://drive.google.com/folderview?id=0B7Ao1qqJJDHQUjVIN3liUUZNWjg&usp=sharing#list | Mar 25, 2025 | — |