How To Convert Breakpointer .Gff To .Vcf (Need To Understand Format)?

Question

[Raymond301]

I'm using Breakpointer, provided from https://github.com/ruping/Breakpointer However the output claims to be .gff. I've already tried to use the gffToVcf.py module provided by PacBio, however this .gff does not adhere to the same standards expected by PacBio.

Here is an example of the format.

• chr1 Breakpointer Depth-Skewed 45796855 45796898 0.482 + . ID=chr1:45796855;SIZE=44;DEPTH=101;EndsRatio=0.424;StartsRatio=0.457;BinomialScore=1.489;MIS=21;realMIS=0;MISRATE=0.490379;seedseq=TGCCTTTTTCAGCGGCGGTGGAAAC

1. chr1
2. Breakpointer
3. Depth-Skewed
4. 45796955
5. 45797010
6. 3.19
7. +
8. .
9. ID=chr1:45796955;SIZE=56;DEPTH=135;EndsRatio=0.407;StartsRatio=0.588;BinomialScore=1.353;MIS=71;realMIS=3;MISRATE=1.2922;seedseq=ATACTTGAGATGTCAGCTTGATCTG

I'd like to convert this to VCF: http://www.1000genomes.org/wiki/analysis/vcf4.0 So I need to figure out how the Breakpointer output maps to

1. #CHROM
2. POS
3. ID
4. REF
5. ALT
6. QUAL
7. FILTER
8. INFO

I'm sure I can script the convert myself, I just need to know what the Breakpointer notes (#9) are since that information is not available in a readme. MIS, realMIS, MISRATE, Ratio?

[PoGibas]

I have the same problem, have you been able to solve it?

[Istvan Albert]

I've sent the author a message via the request help link above.