.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH ESTIMATEERROR.PY "1" "May 2020" "EstimateError.py 0.6.0" "User Commands"
.SH NAME
EstimateError.py \- Calculates annotation set error rates
.SH DESCRIPTION
usage: EstimateError.py [\-\-version] [\-h]  ...
.PP
Calculates annotation set error rates
.SS "help:"
.TP
\fB\-\-version\fR
show program's version number and exit
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.SS "subcommands:"
.IP
Estimation method
.TP
set
Estimates error statistics within annotation sets.
.TP
barcode
Calculates pairwise distance metrics of barcode sequences.
.SS "output files:"
.IP
error\-position
.IP
estimated error by read position.
.IP
error\-quality
.IP
estimated error by the quality score assigned within the input file.
.IP
error\-nucleotide
.IP
estimated error by nucleotide.
.IP
error\-set
.IP
estimated error by annotation set size.
.IP
distance\-set
.IP
pairwise hamming distances by annotation set.
.IP
threshold\-set
.IP
thresholds from pairwise hamming distances for annotation sets.
.IP
distance\-barcode
.IP
estimated error by pairwise hamming distances
.IP
threshold\-barcode
.IP
thresholds from pairwise hamming distances for clustering barcodes
.SS "output fields:"
.IP
POSITION
.IP
read position with base zero indexing.
.IP
Q
.IP
Phred quality score.
.IP
OBSERVED
.IP
observed nucleotide value.
.IP
REFERENCE
.IP
consensus nucleotide for the barcode read group.
.IP
SET_COUNT
.IP
barcode read group size.
.IP
REPORTED_Q
.IP
mean Phred quality score reported within the input file for the given
position, quality score, nucleotide or read group.
.IP
MISMATCHES
.IP
count of observed mismatches from consensus for the given position,
quality score, nucleotide or read group.
.IP
OBSERVATIONS
.IP
total count of observed values for each position, quality score,
nucleotide or read group size.
.IP
ERROR
.IP
estimated error rate.
.IP
EMPIRICAL_Q
.IP
estimated error rate converted to a Phred quality score.
.IP
ALL
.IP
histogram (count) of all pairwise distance distribution.
.IP
DTN
.IP
histogram (count) of distance to nearest distribution.
.IP
DISTANCE
.IP
length normalized hamming distance.
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.