Description

Map short-reads to an indexed reference genome

Input

Name
Description
Pattern

0 ()

1 ()

0 ()

1 ()

mismatch_parameter (float)

Minimum probability of the number of mismatches under -D base error rate

double_stranded_library (boolean)

Library preparation method - specify if double stranded else it's assumed single stranded

five_prime_overhang (float)

5'-overhang length parameter

three_prime_overhang (float)

3'-overhang length parameter

deam_rate_double_stranded (float)

Deamination rate in double-stranded stem of a read

deam_rate_single_stranded (float)

Deamination rate in single-stranded ends of a read

indel_rate (float)

Expected rate of indels between reads and reference

Output

Name
Description
Pattern

0 ()

0 ()

Tools

mapad Documentation

An aDNA aware short-read mapper

License: MIT
Authors