Clarification on BCF file format

phatjoe

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#1

Clarification on BCF file format

01-09-2012, 09:56 AM

I have a bcf file with this format.

HTML Code:

ChrM 21 . A T,G,X 0 . DP=3796;I16=3730,0,55,0,135424,4994460,1972,72624,42241,1163355,634,7544,26664,192714,488,4340 PL 0,255,199,255,217,199,255,217,199,199

DP should be the depth for the base called I pressumed. But what does the I16 field which is succeeded with 16 other comma delimited numbers mean?

Also as for PL,these numbers 0,255,199,255,217,199,255,217,199,199 are the likelihood of the alleles to be P(D|AA),P(D|AT),P(D|AG),P(D|AX),P(D|TT),P(D|TG),p(D|TX),p(D|GG),p(D|GX) and p(D|XX) in chronological order,right?

Please enlighten me. I cant seemed to find the link to any page describing the bcf output!

Thanks in advance!
Tags: bcf file, mpileup
jflowers

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#2

01-09-2012, 10:05 AM

Check the documentation under the section "SAMtools/BCFtools specific information" here: http://samtools.sourceforge.net/mpileup.shtml
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phatjoe

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01-09-2012, 05:22 PM

Originally posted by jflowers View Post

Check the documentation under the section "SAMtools/BCFtools specific information" here: http://samtools.sourceforge.net/mpileup.shtml

Overlooked it. Thanks a bunch!
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