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: singlecategory: prerequisiteoptional: Truepattern: */*.fasta- input
- bam or sam files
output
type: mapsource: inputcategory: outputoptional: {}pattern: ./*.pileup
output_bam
type: mapsource: inputcategory: outputoptional: {}pattern: ./*.sorted
Parameters¶
- cap_mapQ_at
cap mapping quality at INT
type: integerdefault: 60optional: True- extra_params
any extra parameters
type: stringdefault: ``optional: True- filter_read_bits
filtering reads with bits in INT
type: integerdefault: 1796optional: True- input_is_SAM
the input is in SAM
type: booleandefault: Falseoptional: True- num_haplotypes
number of haplotypes in the sample (for -c/-g)
type: integerdefault: 2optional: True- out_2nd_best
output the 2nd best call and quality
type: booleandefault: Falseoptional: True- out_GLFv3_format
output in the GLFv3 format (suppressing -c/-i/-s)
type: booleandefault: Falseoptional: True- out_maq_consensus
output the maq consensus sequence
type: booleandefault: Falseoptional: True- phred_prob_indel
phred prob. of an indel in sequencing/prep. (for -c/-g)
type: integerdefault: 40optional: True- print_variants_only
print variants only (for -c)
type: booleandefault: Falseoptional: True- prior_diff_haplotypes
phred prob. of an indel in sequencing/prep. (for -c/-g)
type: floatdefault: 0.001optional: True- prior_indel_haplotypes
number of haplotypes in the sample (for -c/-g)
type: floatdefault: 0.00015optional: True- show_lines_indels
only show lines/consensus with indels
type: booleandefault: Falseoptional: True- simple_pileup_format
simple (yet incomplete) pileup format
type: booleandefault: Falseoptional: True- theta_maq_model
number of haplotypes in the sample (for -c/-g)
type: floatdefault: 0.85optional: True- use_SOAPsnp_model
use the SOAPsnp model for SNP calling
type: booleandefault: Falseoptional: True
miscellaneous¶
- Backend
- ruff
- Author
- Yogini Idnani, Mark Fiers
- Creation date
- Wed Dec 15 17:06:48 2010
- Modification date
- unknown