https://github.com/applicativesystem/bcftools-utility
bactools-utility for dealing with bcf files
https://github.com/applicativesystem/bcftools-utility
bcf bioinformatics genome-alignment genome-alignment-utilites genome-alignments genome-analysis genome-bioinformatics genome-informatics
Last synced: 2 months ago
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bactools-utility for dealing with bcf files
- Host: GitHub
- URL: https://github.com/applicativesystem/bcftools-utility
- Owner: applicativesystem
- License: mit
- Created: 2024-08-22T19:09:36.000Z (10 months ago)
- Default Branch: main
- Last Pushed: 2024-08-22T19:40:37.000Z (10 months ago)
- Last Synced: 2024-12-16T02:12:10.226Z (6 months ago)
- Topics: bcf, bioinformatics, genome-alignment, genome-alignment-utilites, genome-alignments, genome-analysis, genome-bioinformatics, genome-informatics
- Language: Python
- Homepage:
- Size: 113 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# bcftools-filter
- making bcftools filtering easy. implementation of the bcftools which will allow for the faster filtering of the variant calls according to the allelic depth and the tags using simple to overlap approaches as compared to implementing the regular patterns.
- a bcf filter for filtering the variants and it parses the variants in a flash of a minute.
- you can filter the variants according to the svtype, filter_type, position, allelicdepth, readdepth and chromosome.
- A complete human genome parsed in less than 1 minute the link to the data is also given.
```
bcffiler(bcf_file="/Users/gauravsablok/Desktop/CodeCheck/broad/hs37d5.HG002-SequelII-CCS.bnd-only.sv.vcf",
svtype = "DUP",readdepth = "21")
1 10448 pbsv.BND.1:10448-10:135524737 C C]10:135524737] . NearReferenceGap SVTYPE=INV;CIPOS=-9,20;MATEID=pbsv.BND.10:135524737-1:10448 GT:AD:DP 0/1:27,3:30 GT AD DP structural_type CIPOS mateID
1 1 1584767.0 pbsv.BND.1:1584767-hs37d5:12063285 C C[hs37d5:12063285[ . Decoy SVTYPE=DUP;CIPOS=0,1;MATEID=pbsv.BND.hs37d5:12... GT:AD:DP 0/1:16,5:21 [0, 1] 16,5 21 DUP [CIPOS, 0,1] [MATEID, pbsv.BND.hs37d5:12063285-1:1584767]
2 1 2368006.0 pbsv.BND.1:2368006-hs37d5:6505668 C C]hs37d5:6505668] . Decoy SVTYPE=DUP;CIPOS=-35,36;MATEID=pbsv.BND.hs37d5... GT:AD:DP 0/1:9,2:11 [0, 1] 9,2 11 DUP [CIPOS, -35,36] [MATEID, pbsv.BND.hs37d5:6505668-1:2368006]
bcffiler(bcf_file="/Users/gauravsablok/Desktop/CodeCheck/broad/hs37d5.HG002-SequelII-CCS.bnd-only.sv.vcf", svtype = "DUP")
1 10448 pbsv.BND.1:10448-10:135524737 C C]10:135524737] . NearReferenceGap SVTYPE=INV;CIPOS=-9,20;MATEID=pbsv.BND.10:135524737-1:10448 GT:AD:DP 0/1:27,3:30 GT AD DP structural_type CIPOS mateID
1 1 1584767.0 pbsv.BND.1:1584767-hs37d5:12063285 C C[hs37d5:12063285[ . Decoy SVTYPE=DUP;CIPOS=0,1;MATEID=pbsv.BND.hs37d5:12... GT:AD:DP 0/1:16,5:21 [0, 1] 16,5 21 DUP [CIPOS, 0,1] [MATEID, pbsv.BND.hs37d5:12063285-1:1584767]
2 1 2368006.0 pbsv.BND.1:2368006-hs37d5:6505668 C C]hs37d5:6505668] . Decoy SVTYPE=DUP;CIPOS=-35,36;MATEID=pbsv.BND.hs37d5... GT:AD:DP 0/1:9,2:11 [0, 1] 9,2 11 DUP [CIPOS, -35,36] [MATEID, pbsv.BND.hs37d5:6505668-1:2368006]
```
Gaurav Sablok \
University of Potsdam \
Potsdam,Germany