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24 bytes added ,  17:32, 5 February 2013
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# # READS : Total # of reads loaded from the BAM file
 
# # READS : Total # of reads loaded from the BAM file
 
# # AVG_DP : Average sequencing depth at the sites in the VCF file
 
# # AVG_DP : Average sequencing depth at the sites in the VCF file
# FREEMIX : Sequence-only estimate of contamination
+
# FREEMIX : Sequence-only estimate of contamination (0-1 scale)
 
# FREELK1 : Maximum log-likelihood of the sequence reads given estimated contamination under sequence-only method
 
# FREELK1 : Maximum log-likelihood of the sequence reads given estimated contamination under sequence-only method
 
# FREELK0 : Log-ikelihood of the sequence reads given no contamination under sequence-only method
 
# FREELK0 : Log-ikelihood of the sequence reads given no contamination under sequence-only method
 
# FREE_RH : Estimated reference bias parameter Pr(refBase|HET) (when --free-refBias or --free-full is used)
 
# FREE_RH : Estimated reference bias parameter Pr(refBase|HET) (when --free-refBias or --free-full is used)
 
# FREE_RA : Estimated reference bias parameter Pr(refBase|HOMALT) (when --free-refBias or --free-full is used)
 
# FREE_RA : Estimated reference bias parameter Pr(refBase|HOMALT) (when --free-refBias or --free-full is used)
# CHIPMIX : Sequence+array estimate of contamination (NA if the external genotype is unavailable)
+
# CHIPMIX : Sequence+array estimate of contamination (NA if the external genotype is unavailable) (0-1 scale)
 
# CHIPLK1 : Maximum log-likelihood of the sequence reads given estimated contamination under sequence+array method (NA if the external genotypes are unavailable)
 
# CHIPLK1 : Maximum log-likelihood of the sequence reads given estimated contamination under sequence+array method (NA if the external genotypes are unavailable)
 
# CHIPLK0 : Log-likelihood of the sequence reads given no contamination under sequence+array method (NA if the external genotypes are unavailable)
 
# CHIPLK0 : Log-likelihood of the sequence reads given no contamination under sequence+array method (NA if the external genotypes are unavailable)

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