https://github.com/lpantano/custom_genome_annotation
some annotation that are not that standard but still useful
https://github.com/lpantano/custom_genome_annotation
Last synced: 3 months ago
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some annotation that are not that standard but still useful
- Host: GitHub
- URL: https://github.com/lpantano/custom_genome_annotation
- Owner: lpantano
- License: mit
- Created: 2016-05-24T17:41:13.000Z (about 9 years ago)
- Default Branch: master
- Last Pushed: 2016-08-10T18:03:28.000Z (almost 9 years ago)
- Last Synced: 2025-01-24T23:48:11.754Z (4 months ago)
- Size: 10.3 MB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# custom_genome_annotation
some annotation that are not that standard but still useful
## qsignature hg38
```
awk '{print $1"\t"$2"\t"$2+1"\t"$3"\t"$4}' qsignature.vcf > qsignature.bed
CrossMap.py bed hg19ToHg38.over.chain.gz qsignature.bed qsignature.hg38.bed
awk '{print $1"\t"$2"\t"$4"\t"$5}' qsignature.hg38.bed > qsignature.hg38.txt
```
## acmg56
```
wget https://raw.githubusercontent.com/lpantano/chrom_map/master/chrom_map.py
python chrom_map.py --name GRCh37_ensembl2UCSC --input acmg56.GRCh37.bed --out acmg56.ucsc.bed
CrossMap.py bed ../qsignature/hg19ToHg38.over.chain.gz acmg56.ucsc.bed acmg56.ucsc.hg38.bed
```