https://github.com/poisonalien/somatic_pipeline
https://github.com/poisonalien/somatic_pipeline
Last synced: about 1 month ago
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- Host: GitHub
- URL: https://github.com/poisonalien/somatic_pipeline
- Owner: PoisonAlien
- Created: 2016-02-12T05:38:26.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2021-01-11T12:35:02.000Z (over 4 years ago)
- Last Synced: 2025-04-15T19:08:55.277Z (about 1 month ago)
- Language: Python
- Size: 199 KB
- Stars: 2
- Watchers: 2
- Forks: 4
- Open Issues: 1
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Metadata Files:
- Readme: README.md
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README
###This is the repository of code used for alignment and variant detection for APL sequencing project.
Madan, V., et al., Comprehensive mutational analysis of primary and relapse acute promyelocytic leukemia. Leukemia, 2016. doi: 10.1038/leu.2016.69. PMID: [27063598](https://www.ncbi.nlm.nih.gov/pubmed/27063598)
#### Parameters used for alignment and variant detection are hardcoded into the script. May have to edit accordingly.
#### Alignment:
Assumes bwa, samblaster, sambaba and samtools are under path.
Edit paths for faidx indexed reference genome, gatk jar file, known indels (from gatk [bundle](ftp://ftp.broadinstitute.org/bundle/2.8/hg19/)) and exome baits manually. (From line 15 to 26)
```bash
$ fqtobam.py sample_id sample_name sample_library fq1.gz fq2.gz
```
#### Variant calling using VarScan2:
Assuems samtools and [bam-readcount](https://github.com/genome/bam-readcount) are installed under path.
Edit paths for faidx indexed reference genome, varscan2 jar file, [fpFilter](https://github.com/ckandoth/variant-filter) perl script maunally. (From line 15 to 18)
```bash
$ bash run_varScan.sh normal.bam tumor.bam basename
```