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# RG : ReadGroup ID of sequenced lane. For [outPrefix].selfSM and [outPrefix].bestSM, these values are "ALL"
# RG : ReadGroup ID of sequenced lane. For [outPrefix].selfSM and [outPrefix].bestSM, these values are "ALL"
* CHIP_ID : Sample ID compared to in the genotype file. For [outPrefix].selfRG and [outPrefix].selfSM, these values should be identical to [SEQ_SM] or "NA" if the genotype of sequenced samples are unavailable. For [outPrefix].bestRG and [outPrefix].bestSM, these values should be the ID of best-matching sample among the genotype files compared to.
* CHIP_ID : Sample ID compared to in the genotype file. For [outPrefix].selfRG and [outPrefix].selfSM, these values should be identical to [SEQ_SM] or "NA" if the genotype of sequenced samples are unavailable. For [outPrefix].bestRG and [outPrefix].bestSM, these values should be the ID of best-matching sample among the genotype files compared to.
# # SNPs : # of SNPs passing the criteria from the VCF file
# # READS : Total # of reads loaded from the BAM file
# # AVG_DP : Average sequencing depth at the sites in the VCF file
# FREEMIX : Sequence-only estimate of contamination
# 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
# 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)
# CHIPMIX : Sequence+array estimate of contamination (NA if the external genotype is 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)
# CHIP_RH : Estimated reference bias parameter Pr(refBase|HET) (when --chip-refBias or --chip-full is used)
# CHIP_RA : Estimated reference bias parameter Pr(refBase|HOMALT) (when --chip-refBias or --chip-full is used)
# DPREF : Depth (Coverage) of HomRef site (based on the genotypes of (SELF_SM/BEST_SM), passing mapQ, baseQual, maxDepth thresholds.
# DPREF : Depth (Coverage) of HomRef site (based on the genotypes of (SELF_SM/BEST_SM), passing mapQ, baseQual, maxDepth thresholds.
# RDPHET : DPHET/DPREF, Relative depth at Heterozygous site.
# RDPHET : DPHET/DPREF, Relative depth at Heterozygous site.
