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Illumina / manta

Structural variant and indel caller for mapped sequencing data
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Depth and Allele frequency calculations #228

Open Nitin123-4 opened 4 years ago

Nitin123-4 commented 4 years ago

Is there any formula to get below from Manta VCF:

Alt_Depth BP1_Depth BP2_Depth Total_Depth VAF

Example Manta VCF:

chr2 42522715 MantaBND:1695:1:5:0:0:0:1 C C]chr2:29447256] . PASS SVTYPE=BND;MATEID=MantaBND:1695:1:5:0:0:0:0;CONTIG=GATCTGTGCTCTAATTCCGCCTCTTGTTACTTACAAGCTGAGCCATGAGGACCAGGTCACAGGACCTCTTTGGACTGCAGTTTCCCTCTCTGTAGGCAGGGATGGTAACTCCTGCCCTGTTTCCCTAACCACTGGACTGAAAGAGTACTATGTGAGAATTACCAGAAATGAGTTTAATATAAGAATACTGTACCTTTAGGTCCTTTCCCAGGTGTGGGCTCTACAGTAGTTTTGCTCCATATAAGCATGACTCCACCTGAGTCTCCAGTAAGAACATCTCCATTCCCCAAGAATGCTAAACACTGCACAAATTTTGGCT;CIPOS=0,1;HOMLEN=1;HOMSEQ=C;BND_DEPTH=1758;MATE_BND_DEPTH=6281 PR:SR 668,0:3766,90

chr2 | 29447255 | MantaBND:1695:1:5:0:0:0:0 | T | T]chr2:42522716] | . | PASS | SVTYPE=BND;MATEID=MantaBND:1695:1:5:0:0:0:1;CONTIG=GATCTGTGCTCTAATTCCGCCTCTTGTTACTTACAAGCTGAGCCATGAGGACCAGGTCACAGGACCTCTTTGGACTGCAGTTTCCCTCTCTGTAGGCAGGGATGGTAACTCCTGCCCTGTTTCCCTAACCACTGGACTGAAAGAGTACTATGTGAGAATTACCAGAAATGAGTTTAATATAAGAATACTGTACCTTTAGGTCCTTTCCCAGGTGTGGGCTCTACAGTAGTTTTGCTCCATATAAGCATGACTCCACCTGAGTCTCCAGTAAGAACATCTCCATTCCCCAAGAATGCTAAACACTGCACAAATTTTGGCT;CIPOS=0,1;HOMLEN=1;HOMSEQ=G;BND_DEPTH=6281;MATE_BND_DEPTH=1758 | PR:SR | 668,0:3766,90

garrettlew2691 commented 3 years ago

Please add these as key-value pairs to info.