samtools_pileup

Print the alignment in the pileup format.

Commands

clean
Remove all job data, not the Moa job itself
run
run samtools pileup command

Filesets

fasta

reference fasta file

type: single
category: prerequisite
optional: True
pattern: */*.fasta
input
bam or sam files

output

type: map
source: input
category: output
optional: {}
pattern: ./*.pileup

output_bam

type: map
source: input
category: output
optional: {}
pattern: ./*.sorted

Parameters

cap_mapQ_at

cap mapping quality at INT

type: integer
default: 60
optional: True
extra_params

any extra parameters

type: string
default: ``
optional: True
filter_read_bits

filtering reads with bits in INT

type: integer
default: 1796
optional: True
input_is_SAM

the input is in SAM

type: boolean
default: False
optional: True
num_haplotypes

number of haplotypes in the sample (for -c/-g)

type: integer
default: 2
optional: True
out_2nd_best

output the 2nd best call and quality

type: boolean
default: False
optional: True
out_GLFv3_format

output in the GLFv3 format (suppressing -c/-i/-s)

type: boolean
default: False
optional: True
out_maq_consensus

output the maq consensus sequence

type: boolean
default: False
optional: True
phred_prob_indel

phred prob. of an indel in sequencing/prep. (for -c/-g)

type: integer
default: 40
optional: True
print_variants_only

print variants only (for -c)

type: boolean
default: False
optional: True
prior_diff_haplotypes

phred prob. of an indel in sequencing/prep. (for -c/-g)

type: float
default: 0.001
optional: True
prior_indel_haplotypes

number of haplotypes in the sample (for -c/-g)

type: float
default: 0.00015
optional: True
show_lines_indels

only show lines/consensus with indels

type: boolean
default: False
optional: True
simple_pileup_format

simple (yet incomplete) pileup format

type: boolean
default: False
optional: True
theta_maq_model

number of haplotypes in the sample (for -c/-g)

type: float
default: 0.85
optional: True
use_SOAPsnp_model

use the SOAPsnp model for SNP calling

type: boolean
default: False
optional: True

miscellaneous

Backend
ruff
Author
Yogini Idnani, Mark Fiers
Creation date
Wed Dec 15 17:06:48 2010
Modification date
unknown