EstimateError.py1
Calculates annotation set error rates
Overview
usage: EstimateError.py [--version] [-h] ...
Calculates annotation set error rates
help:
-
--version -
show program's version number and exit
-
-h, --help -
show this help message and exit
subcommands:
|
Estimation method |
|
set
|
Estimates error statistics within annotation sets. |
barcode
|
Calculates pairwise distance metrics of barcode sequences. |
output files:
|
error-position |
|
|
estimated error by read position. |
|
|
error-quality |
|
|
estimated error by the quality score assigned within the input file. |
|
|
error-nucleotide |
|
|
estimated error by nucleotide. |
|
|
error-set |
|
|
estimated error by annotation set size. |
|
|
distance-set |
|
|
pairwise hamming distances by annotation set. |
|
|
threshold-set |
|
|
thresholds from pairwise hamming distances for annotation sets. |
|
|
distance-barcode |
|
|
estimated error by pairwise hamming distances |
|
|
threshold-barcode |
|
|
thresholds from pairwise hamming distances for clustering barcodes |
output fields:
-
POSITION
-
read position with base zero indexing.
-
Q
-
Phred quality score.
-
OBSERVED
-
observed nucleotide value.
-
REFERENCE
-
consensus nucleotide for the barcode read group.
-
SET_COUNT
-
barcode read group size.
-
REPORTED_Q
-
mean Phred quality score reported within the input file for the given position, quality score, nucleotide or read group.
-
MISMATCHES
-
count of observed mismatches from consensus for the given position, quality score, nucleotide or read group.
-
OBSERVATIONS
-
total count of observed values for each position, quality score, nucleotide or read group size.
-
ERROR
-
estimated error rate.
-
EMPIRICAL_Q
-
estimated error rate converted to a Phred quality score.
-
ALL
-
histogram (count) of all pairwise distance distribution.
-
DTN
-
histogram (count) of distance to nearest distribution.
-
DISTANCE
-
length normalized hamming distance.
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).