Hallo,
I'd like to understand how to covert the VP INFO field of a VCF file into the binary number. My question has to some extend been discussed here:
http://www.biostars.org/post/show/38...eld-structure/
Here is the explanation how to interpret the VP field. ftp://ftp.ncbi.nlm.nih.gov/snp/specs...eld_latest.pdf
Here is a line from a dbSNP file.
1 10144 rs144773400 TA T . . RSPOS=10145;dbSNPBuildID=134;SSR=0;SAO=0;VP=050000000005000002000200;WGT=1;VC=DIV;ASP;OTHERKG
I am interested in other fields than the WGT, VC, R5, and ASP, which give some of the information in VP already decoded.
Especially, I am interested in the byte F4 that corresponds to the allele frequency proportions. From what I understand, this number needs to be converted to a binary number to read the bits, however, what is unclear to me is the number system in the VP number is in. In the post mentionend obove, a user gave a number that had "a" in it so it must be a number system greater 11, maybe hexadecimal? the VP number corresponds to a 12 byte object, so we should obtain 96 bits if the number is decoded. However, if I assume that the VP number is hexadecimal and I convert to binary, I obtain 91 bits. Also decimal or octal does not match.
Another point: Is the whole number converted as one? The VP number has 24 characters. Maybe two characters at a time correspond to one byte. So I would have to convert only 00 to get my F4 byte?! but then again, what number system is 00 in?
Does somebody know the answer? Thanks.
I'd like to understand how to covert the VP INFO field of a VCF file into the binary number. My question has to some extend been discussed here:
http://www.biostars.org/post/show/38...eld-structure/
Here is the explanation how to interpret the VP field. ftp://ftp.ncbi.nlm.nih.gov/snp/specs...eld_latest.pdf
Here is a line from a dbSNP file.
1 10144 rs144773400 TA T . . RSPOS=10145;dbSNPBuildID=134;SSR=0;SAO=0;VP=050000000005000002000200;WGT=1;VC=DIV;ASP;OTHERKG
I am interested in other fields than the WGT, VC, R5, and ASP, which give some of the information in VP already decoded.
Especially, I am interested in the byte F4 that corresponds to the allele frequency proportions. From what I understand, this number needs to be converted to a binary number to read the bits, however, what is unclear to me is the number system in the VP number is in. In the post mentionend obove, a user gave a number that had "a" in it so it must be a number system greater 11, maybe hexadecimal? the VP number corresponds to a 12 byte object, so we should obtain 96 bits if the number is decoded. However, if I assume that the VP number is hexadecimal and I convert to binary, I obtain 91 bits. Also decimal or octal does not match.
Another point: Is the whole number converted as one? The VP number has 24 characters. Maybe two characters at a time correspond to one byte. So I would have to convert only 00 to get my F4 byte?! but then again, what number system is 00 in?
Does somebody know the answer? Thanks.
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