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, 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) |