MutationFilter

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 the percentage of reads 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 --low_mapq_cutoff 10 --low_mapq_pct 15

• • Filter based on low Map Quality (LMQ): filtered if the percentage of reads 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 --low_mapq_cutoff 10 --mut_low_mapq_pct 10

• Filter based on low Base Quality (LMQ): filtered if the percentage of reads 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  --low_baseq_cutoff 30 --mut_low_baseq_pct 50