MCHap
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Additional info fields
Some additional (optional) info fields that would speed up filtering etc.
-
MCIP
/MCIT
: proportion/count of samples found with evidence of Markov chain incongruence -
SAFP
: sum of posterior allele frequencies (less issue with rounding in larger populations) -
SAOP
sum of posterior allele occurrence (interpreted as number of samples in which an allele occurs) -
CIGAR
(lengthA
): alternative toSNVPOS
-
NLOC
: number of variable loci (count of values inSNVPOS
) -
UAN
: Count of unique in state alleles