- 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