Difference between revisions of "MutationFilter"
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When filters have 'mut_' the filters are for the statistis calculated for MUTANT alleles only! | When filters have 'mut_' the filters are for the statistis calculated for MUTANT alleles only! | ||
| − | * | + | * Some examples |
| + | mutfilter --bam in.bam --bed in.bed --indel_winsize 20 --indel_cnt 3 | ||
| + | mutfilter --bam in.bam --bed in.bed --indel_winsize 20 --indel_cnt 3 --mut_median_cycles2ends 5 | ||
| + | mutfilter --bam in.bam --bed in.bed --indel_winsize 20 --indel_cnt 3 --mut_median_cycles2ends 5 --mut_clip_pct 20 | ||
| + | mutfilter --bam in.bam --bed in.bed --indel_winsize 20 --indel_cnt 3 --mut_median_cycles2ends 5 --mut_clip_pct 20 --mut_base_pct 30 | ||
| + | mutfilter --bam in.bam --bed in.bed --indel_winsize 20 --indel_cnt 3 --mut_median_cycles2ends 5 --mut_clip_pct 20 --mut_base_pct 30 --low_mapq_cutoff 10 --low_mapq_pct 10 | ||
| + | mutfilter --bam in.bam --bed in.bed --indel_winsize 20 --indel_cnt 3 --mut_median_cycles2ends 5 --mut_clip_pct 20 --mut_base_pct 30 --low_mapq_cutoff 10 --low_mapq_pct 10 --mut_low_mapq_pct 10 | ||
| + | mutfilter --bam in.bam --bed in.bed --indel_winsize 20 --indel_cnt 3 --mut_median_cycles2ends 5 --mut_clip_pct 20 --mut_base_pct 30 --low_baseq_cutoff 10 --low_baseq_pct 10 --mut_low_baseq_pct 10 | ||
Revision as of 13:38, 1 April 2013
Introduction
- The tool mutfilter generates various diagnosis statistics based on sequence alignment and filters alignment artifacts based on user-provided criteria.
- It takes as input a SAM/BAM file (through --bam) and a BED-like file (through --bed) and generates output on screen.
- Additional filtering options can be provided and mutfilter will generate filtering flags for each input filtering option. See details below.
Usage
- Typing mutfiler without any other options will display the following message
The following parameters are available. Ones with "[]" are in effect:
Input Files : --bam [], --bed []
Cycle Bias (CB) : --mut_median_cycles2ends [-1]
Strand Bias (SB) : --SB_OR [-1.0e+00]
Nearby Indels (INDEL) : --indel_winsize [30], --indel_cnt [-1],
--indel_pct [-1.0e+00]
Head Clip (HC) : --mut_clip_cnt [-1], --mut_clip_pct [-1.0e+00]
Other Alleles (OA) : --other_allele_cnt [-1],
--other_allele_pct [-1.0e+00]
Allelic Balance (AB) : --mut_base_cnt [-1], --mut_base_pct [-1.0e+00]
Low Map Quality (LMQ) : --low_mapq_cutoff [-1.0e+00], --low_mapq_cnt [-1],
--low_mapq_pct [-1.0e+00], --mut_low_mapq_cnt [-1],
--mut_low_mapq_pct [-1.0e+00]
Low Base Quality (LBQ) : --low_baseq_cutoff [-1.0e+00],
--low_baseq_cnt [-1], --low_baseq_pct [-1.0e+00],
--mut_low_baseq_cnt [-1],
--mut_low_baseq_pct [-1.0e+00]
Improper Paired (IP) : --improper_paried_cnt [-1],
--improper_paried_pct [-1.0e+00],
--mut_improper_paried_cnt [-1],
--mut_improper_paried_pct [-1.0e+00]
NOTE: When parameters are negative these filters are NOT in effect!
When filters have 'mut_' the filters are for the statistis calculated for MUTANT alleles only!
- Some examples
mutfilter --bam in.bam --bed in.bed --indel_winsize 20 --indel_cnt 3 mutfilter --bam in.bam --bed in.bed --indel_winsize 20 --indel_cnt 3 --mut_median_cycles2ends 5 mutfilter --bam in.bam --bed in.bed --indel_winsize 20 --indel_cnt 3 --mut_median_cycles2ends 5 --mut_clip_pct 20 mutfilter --bam in.bam --bed in.bed --indel_winsize 20 --indel_cnt 3 --mut_median_cycles2ends 5 --mut_clip_pct 20 --mut_base_pct 30 mutfilter --bam in.bam --bed in.bed --indel_winsize 20 --indel_cnt 3 --mut_median_cycles2ends 5 --mut_clip_pct 20 --mut_base_pct 30 --low_mapq_cutoff 10 --low_mapq_pct 10 mutfilter --bam in.bam --bed in.bed --indel_winsize 20 --indel_cnt 3 --mut_median_cycles2ends 5 --mut_clip_pct 20 --mut_base_pct 30 --low_mapq_cutoff 10 --low_mapq_pct 10 --mut_low_mapq_pct 10 mutfilter --bam in.bam --bed in.bed --indel_winsize 20 --indel_cnt 3 --mut_median_cycles2ends 5 --mut_clip_pct 20 --mut_base_pct 30 --low_baseq_cutoff 10 --low_baseq_pct 10 --mut_low_baseq_pct 10
