MutationFilter - Revision history

Bingshan: /* 6. 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% */

2013-04-16T05:06:12Z

6. 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%

← Older revision		Revision as of 01:06, 16 April 2013
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	===== 6. 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% =====		===== 6. 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		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 15

	===== 7. Filter based on low Base Quality (LBQ): 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% =====		===== 7. Filter based on low Base Quality (LBQ): 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% =====

Bingshan: /* Download */

2013-04-12T17:38:53Z

Download

← Older revision		Revision as of 13:38, 12 April 2013
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	=== Download ===		=== Download ===
	~~[[media: \| Download]]~~
	Source code can be [[Media:Mutfilter.tar.gz \| Downloaded]] here.		Source code can be [[Media:Mutfilter.tar.gz \| Downloaded]] here.

Bingshan at 17:38, 12 April 2013

2013-04-12T17:38:02Z

← Older revision		Revision as of 13:38, 12 April 2013
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	*meanBQ_pass: average of BaseQ of reads that have BaseQ > low_baseq_cutoff.		*meanBQ_pass: average of BaseQ of reads that have BaseQ > low_baseq_cutoff.
	*mut_meanBQ_pass: average of BaseQ of mutant alleles that have BaseQ > low_baseq_cutoff.		*mut_meanBQ_pass: average of BaseQ of mutant alleles that have BaseQ > low_baseq_cutoff.

			=== Download ===
			[[media: \| Download]]
			Source code can be [[Media:Mutfilter.tar.gz \| Downloaded]] here.

Bingshan at 16:01, 12 April 2013

2013-04-12T16:01:20Z

← Older revision		Revision as of 12:01, 12 April 2013
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	*nMut: # of MUT alleles		*nMut: # of MUT alleles
	*nOA: # of other alleles different from REF and MUT alleles.		*nOA: # of other alleles different from REF and MUT alleles.
	*MP:MM:RP:RM: #~~Mut~~ on ~~plus~~ strand : #~~Mut~~ on ~~minus~~ strand : #~~Ref~~ on ~~plus~~ strand : #~~Ref~~ on ~~minus~~ strand		*RF:RR:MF:MR: #Ref on forward strand : #Ref on reverse strand : #Mut on forward strand : #Mut on reverse strand
	*nINS: # of reads with insertions in a window of sized specified by --indel_winsize		*nINS: # of reads with insertions in a window of sized specified by --indel_winsize
	*nDEL: # of reads with deletions in a window as nINS		*nDEL: # of reads with deletions in a window as nINS
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	*nLBQ: # of low quality bases		*nLBQ: # of low quality bases
	*nLBQ_mut: # of low quality mutant bases.		*nLBQ_mut: # of low quality mutant bases.
			*meanMQ_pass: average of MapQ of reads that have MapQ > low_mapq_cutoff.
			*mut_meanMQ_pass: average of MapQ of reads that have MapQ > low_mapq_cutoff AND contain the mutant allele.
			*meanBQ_pass: average of BaseQ of reads that have BaseQ > low_baseq_cutoff.
			*mut_meanBQ_pass: average of BaseQ of mutant alleles that have BaseQ > low_baseq_cutoff.

Bingshan at 18:34, 1 April 2013

2013-04-01T18:34:07Z

← Older revision		Revision as of 14:34, 1 April 2013
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	=== Input ===		=== Input ===
	* SAM/BAM file		* [[http://samtools.sourceforge.net/ SAM/BAM]] file
	* BED-like file: It requires 5 columns as CHR, START, END, REF, MUTANT in that order. It also requires that START=END here since it deal with single sites		* BED-like file: It requires 5 columns as CHR, START, END, REF, MUTANT in that order. It also requires that START=END here since it deal with single sites

Bingshan at 18:31, 1 April 2013

2013-04-01T18:31:58Z

← Older revision		Revision as of 14:31, 1 April 2013
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	The first 5 columns are the same as the input BED-like file. The following columns are various statistics based on which various filtering can be achieved. The meaning of each column is as follows		The first 5 columns are the same as the input BED-like file. The following columns are various statistics based on which various filtering can be achieved. The meaning of each column is as follows
	*FILTER: indicates the filtering criteria a candidate failed, separated by commas. A '.' is used if not set.		*FILTER: indicates the filtering criteria a candidate failed, separated by commas. A . is used if not set.
	*nRef: # of REF alleles		*nRef: # of REF alleles
	*nMut: # of MUT alleles		*nMut: # of MUT alleles
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	*nClip_mut: # of reads with clipping from the head of reads		*nClip_mut: # of reads with clipping from the head of reads
	*Cycle_mut: the median distance of the mutation allele to the nearest end of a read		*Cycle_mut: the median distance of the mutation allele to the nearest end of a read
	*SB: strand bias odds ratio, which can be derived from MP:MM:RP:RM. A '.' is used if not applicable (e.g. all are on the same strand).		*SB: strand bias odds ratio, which can be derived from MP:MM:RP:RM. A . is used if not applicable (e.g. all are on the same strand).
	*nIP: # of improperly paired reads		*nIP: # of improperly paired reads
	*nIP_mut: # of improperly paired reads carrying the mutant allele		*nIP_mut: # of improperly paired reads carrying the mutant allele

Bingshan at 18:31, 1 April 2013

2013-04-01T18:31:41Z

← Older revision		Revision as of 14:31, 1 April 2013
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	The first 5 columns are the same as the input BED-like file. The following columns are various statistics based on which various filtering can be achieved. The meaning of each column is as follows		The first 5 columns are the same as the input BED-like file. The following columns are various statistics based on which various filtering can be achieved. The meaning of each column is as follows
	*FILTER: indicates the filtering criteria a candidate failed, separated by commas		*FILTER: indicates the filtering criteria a candidate failed, separated by commas. A '.' is used if not set.
	*nRef: # of REF alleles		*nRef: # of REF alleles
	*nMut: # of MUT alleles		*nMut: # of MUT alleles
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	*nClip_mut: # of reads with clipping from the head of reads		*nClip_mut: # of reads with clipping from the head of reads
	*Cycle_mut: the median distance of the mutation allele to the nearest end of a read		*Cycle_mut: the median distance of the mutation allele to the nearest end of a read
	*SB: strand bias odds ratio, which can be derived from MP:MM:RP:RM		*SB: strand bias odds ratio, which can be derived from MP:MM:RP:RM. A '.' is used if not applicable (e.g. all are on the same strand).
	*nIP: # of improperly paired reads		*nIP: # of improperly paired reads
	*nIP_mut: # of improperly paired reads carrying the mutant allele		*nIP_mut: # of improperly paired reads carrying the mutant allele

Bingshan at 18:28, 1 April 2013

2013-04-01T18:28:53Z

Bingshan at 18:28, 1 April 2013

2013-04-01T18:28:21Z

← Older revision		Revision as of 14:28, 1 April 2013
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	The first 5 columns are the same as the input BED-like file. The following columns are various statistics based on which various filtering can be achieved. The meaning of each column is as follows		The first 5 columns are the same as the input BED-like file. The following columns are various statistics based on which various filtering can be achieved. The meaning of each column is as follows
	FILTER: indicates the filtering criteria a candidate failed, separated by commas		*FILTER: indicates the filtering criteria a candidate failed, separated by commas
	nRef: # of REF alleles		*nRef: # of REF alleles
	nMut: # of MUT alleles		nMut: # of MUT alleles
	nOA: # of other alleles different from REF and MUT alleles.		nOA: # of other alleles different from REF and MUT alleles.

Bingshan at 18:28, 1 April 2013

2013-04-01T18:28:00Z

← Older revision		Revision as of 14:28, 1 April 2013
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	#CHR START END REF MUT FILTER nRef nMut nOA MP:MM:RP:RM nINS nDEL nClip_mut Cycle_mut SB nIP nIP_mut nLMQ nLMQ_mut nLBQ nLBQ_mut		#CHR START END REF MUT FILTER nRef nMut nOA MP:MM:RP:RM nINS nDEL nClip_mut Cycle_mut SB nIP nIP_mut nLMQ nLMQ_mut nLBQ nLBQ_mut
	11 190324 190324 A C BQM 0 5 0 2:3:0:0 0 1 0 20 . 0 0 0 0 5 5		11 190324 190324 A C INDEL,AB,BQM 0 5 0 2:3:0:0 0 1 0 20 . 0 0 0 0 5 5

			The first 5 columns are the same as the input BED-like file. The following columns are various statistics based on which various filtering can be achieved. The meaning of each column is as follows
			FILTER: indicates the filtering criteria a candidate failed, separated by commas
			nRef: # of REF alleles
			nMut: # of MUT alleles
			nOA: # of other alleles different from REF and MUT alleles.
			MP:MM:RP:RM: #Mut on plus strand : #Mut on minus strand : #Ref on plus strand : #Ref on minus strand
			nINS: # of reads with insertions in a window of sized specified by --indel_winsize
			nDEL: # of reads with deletions in a window as nINS
			nClip_mut: # of reads with clipping from the head of reads
			Cycle_mut: the median distance of the mutation allele to the nearest end of a read
			SB: strand bias odds ratio, which can be derived from MP:MM:RP:RM
			nIP: # of improperly paired reads
			nIP_mut: # of improperly paired reads carrying the mutant allele
			nLMQ: # of reads with low mapping quality
			nLMQ_mut: # of low mapping quality reads that carry the mutant allele
			nLBQ: # of low quality bases
			nLBQ_mut: # of low quality mutant bases.

← Older revision		Revision as of 14:28, 1 April 2013
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	*FILTER: indicates the filtering criteria a candidate failed, separated by commas		*FILTER: indicates the filtering criteria a candidate failed, separated by commas
	*nRef: # of REF alleles		*nRef: # of REF alleles
	nMut: # of MUT alleles		*nMut: # of MUT alleles
	nOA: # of other alleles different from REF and MUT alleles.		*nOA: # of other alleles different from REF and MUT alleles.
	MP:MM:RP:RM: #Mut on plus strand : #Mut on minus strand : #Ref on plus strand : #Ref on minus strand		*MP:MM:RP:RM: #Mut on plus strand : #Mut on minus strand : #Ref on plus strand : #Ref on minus strand
	nINS: # of reads with insertions in a window of sized specified by --indel_winsize		*nINS: # of reads with insertions in a window of sized specified by --indel_winsize
	nDEL: # of reads with deletions in a window as nINS		*nDEL: # of reads with deletions in a window as nINS
	nClip_mut: # of reads with clipping from the head of reads		*nClip_mut: # of reads with clipping from the head of reads
	Cycle_mut: the median distance of the mutation allele to the nearest end of a read		*Cycle_mut: the median distance of the mutation allele to the nearest end of a read
	SB: strand bias odds ratio, which can be derived from MP:MM:RP:RM		*SB: strand bias odds ratio, which can be derived from MP:MM:RP:RM
	nIP: # of improperly paired reads		*nIP: # of improperly paired reads
	nIP_mut: # of improperly paired reads carrying the mutant allele		*nIP_mut: # of improperly paired reads carrying the mutant allele
	nLMQ: # of reads with low mapping quality		*nLMQ: # of reads with low mapping quality
	nLMQ_mut: # of low mapping quality reads that carry the mutant allele		*nLMQ_mut: # of low mapping quality reads that carry the mutant allele
	nLBQ: # of low quality bases		*nLBQ: # of low quality bases
	nLBQ_mut: # of low quality mutant bases.		*nLBQ_mut: # of low quality mutant bases.