BiopetFlagstat

Introduction

This tool has been created to extract all the metrics from a required bam file. It captures for example the # of mapped reads, # of duplicates, # of mates unmapped, # of reads with a certain mapping quality etc. etc.

Example

To get the help menu:

biopet tool BiopetFlagstat -h
Usage: BiopetFlagstat [options]

  -l <value> | --log_level <value>
        Log level
  -h | --help
        Print usage
  -v | --version
        Print version
  -I <file> | --inputFile <file>
        out is a required file property
  -r <chr:start-stop> | --region <chr:start-stop>
        out is a required file property

To run the tool:

biopet tool BiopetFlagstat -I myBAM.bam

Output

Number	Total Flags	Fraction	Name
1	862623034	100.0000%	All
2	861096240	99.8230%	Mapped
3	26506366	3.0728%	Duplicates
4	431233321	49.9909%	FirstOfPair
5	431389713	50.0091%	SecondOfPair
6	430909871	49.9534%	ReadNegativeStrand
7	0	0.0000%	NotPrimaryAlignment
8	862623034	100.0000%	ReadPaired
9	803603283	93.1581%	ProperPair
10	430922821	49.9549%	MateNegativeStrand
11	1584255	0.1837%	MateUnmapped
12	0	0.0000%	ReadFailsVendorQualityCheck
13	1380318	0.1600%	SupplementaryAlignment
14	1380318	0.1600%	SecondaryOrSupplementary
15	821996241	95.2903%	MAPQ>0
16	810652212	93.9753%	MAPQ>10
17	802852105	93.0710%	MAPQ>20
18	789252132	91.4944%	MAPQ>30
19	770426224	89.3120%	MAPQ>40
20	758373888	87.9149%	MAPQ>50
21	0	0.0000%	MAPQ>60
22	835092541	96.8085%	First normal, second read inverted (paired end orientation)
23	765156	0.0887%	First normal, second read normal
24	624090	0.0723%	First inverted, second read inverted
25	11537740	1.3375%	First inverted, second read normal
26	1462857	0.1696%	Mate in same strand
27	11751691	1.3623%	Mate on other chr