---
name: "EstimateError.py"
section: "1"
platform: "linux"
package: "presto"
version: "0.7.2-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/EstimateError.py"
---

# EstimateError.py(1)

Calculates annotation set error rates

## NAME

EstimateError.py - Calculates annotation set error rates

## DESCRIPTION

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.

## AUTHOR

 This manpage was written by Andreas Tille for the Debian distribution and\
  can be used for any other usage of the program.