Difference between revisions of "MutationFilter"
From Genome Analysis Wiki
Jump to navigationJump to searchLine 34: | Line 34: | ||
* Some examples | * Some examples | ||
+ | ** Filter based on nearby Indels (INDEL): filtered if there are >=3 reads with Indels in a window if 20bp up- and down-stream of the mutation candidate. | ||
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 | ||
+ | |||
+ | ** Filter based on cycle bias (CB): filtered if the median distance to the nearest end of the mutant allele is >=5. | ||
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 | ||
+ | |||
+ | ** Filter based on clipped reads (CL): filter if percentage of the reads carrying the mutant allele is >=20% | ||
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 | ||
+ | |||
+ | ** Filter based on Allelic Balance (AB):filtered if the percentage of the reads '''carrying the mutant allele''' is <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 | 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 -- | + | ** Filter based on low Map Quality (LMQ): filtered if percentage of read with low Map quality (defined as map quality below 10 vis --low_mapq_cutoff) is >=15% |
− | 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 | + | 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 15 |
+ | |||
+ | ** Filter based on low Map Quality (LMQ): filtered if percentage of read '''carrying the mutant allele''' with low Map quality (defined as map quality below 10 via --low_mapq_cutoff) is >=15% | ||
+ | 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 --mut_low_mapq_pct 10 | ||
+ | |||
+ | ** Filter based on low Base Quality (LMQ): filtered if percentage of read '''carrying the mutant allele''' with low Base Quality (defined as base quality below 30 via --low_baseq_cutoff) is >=50% | ||
+ | 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 30 --mut_low_baseq_pct 50 |
Revision as of 13:53, 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
- Filter based on nearby Indels (INDEL): filtered if there are >=3 reads with Indels in a window if 20bp up- and down-stream of the mutation candidate.
mutfilter --bam in.bam --bed in.bed --indel_winsize 20 --indel_cnt 3
- Filter based on cycle bias (CB): filtered if the median distance to the nearest end of the mutant allele is >=5.
mutfilter --bam in.bam --bed in.bed --indel_winsize 20 --indel_cnt 3 --mut_median_cycles2ends 5
- Filter based on clipped reads (CL): filter if percentage of the reads carrying the mutant allele is >=20%
mutfilter --bam in.bam --bed in.bed --indel_winsize 20 --indel_cnt 3 --mut_median_cycles2ends 5 --mut_clip_pct 20
- Filter based on Allelic Balance (AB):filtered if the percentage of the reads carrying the mutant allele is <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
- Filter based on low Map Quality (LMQ): filtered if percentage of read with low Map quality (defined as map quality below 10 vis --low_mapq_cutoff) is >=15%
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 15
- Filter based on low Map Quality (LMQ): filtered if percentage of read carrying the mutant allele with low Map quality (defined as map quality below 10 via --low_mapq_cutoff) is >=15%
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 --mut_low_mapq_pct 10
- Filter based on low Base Quality (LMQ): filtered if percentage of read carrying the mutant allele with low Base Quality (defined as base quality below 30 via --low_baseq_cutoff) is >=50%
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 30 --mut_low_baseq_pct 50