bwa_sampe¶

Generate alignments in SAM format given paired end reads

Commands¶

fq_forward_input: fastq input files directory - forward
fq_reverse_input: fastq input files directory - reverse

type: map

source: fq_forward_input

category: input

optional: True

pattern: */*_2.fq

output_bam

type: map

source: fq_forward_input

category: output

optional: {}

pattern: ./*.bam

sai_forward_input: sai input files - forward

type: map

source: fq_forward_input

category: input

optional: False

pattern: */*_1.sai
sai_reverse_input: sai input files - reverse files

type: map

source: sai_forward_input

category: input

optional: True

pattern: */*_2.sai

db: bwa database to align against

type: string

default: {}

optional: False
disable_insert_size: disable insert size estimate (force -s)

type: boolean

default: False

optional: True
disable_SW: disable Smith-Waterman for the unmapped mate

type: boolean

default: False

optional: True
lots_of_data: store unmapped reads - takes up a lot of space!

type: boolean

default: False

optional: True
max_aln_out: maximum hits to output for paired reads

type: integer

default: 3

optional: True
max_insert_size: maximum insert size

type: integer

default: 500

optional: True
max_occ_read: maximum occurrences for one end

type: integer

default: {}

optional: True
max_out_discordant_pairs: maximum hits to output for discordant pairs

type: integer

default: {}

optional: True
preload_index: preload index into memory (for base-space reads only)

type: boolean

default: False

optional: True
prior_chimeric_rate: prior of chimeric rate (lower bound)

type: integer

default: {}

optional: True