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Old 01-09-2012, 08:56 AM   #1
phatjoe
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Question Clarification on BCF file format

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!
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Old 01-09-2012, 09:05 AM   #2
jflowers
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Check the documentation under the section "SAMtools/BCFtools specific information" here: http://samtools.sourceforge.net/mpileup.shtml
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Old 01-09-2012, 04:22 PM   #3
phatjoe
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Quote:
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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