AligFilterFlag

Allows to filter SAM files with alignments using the flag field. The alignment file is split in two based on the value given in the flag parameter. For example if flag=64, the files are split based on if the reads are the first or the second mate of the pair end read. A list of flags can be used as well. Other possible values for flag are:

Bit 0 (1) = The read is one of two or more reads coming from the same fragment during sequencing (e.g. a pair)
Bit 1 (2) = All mate reads are mapped
Bit 2 (4) = The query sequence is unmapped
Bit 3 (8) = The next mate read is unmapped
Bit 4 (16) = Strand of query (0=forward 1=reverse)
Bit 5 (32) = Strand of the next mate read
Bit 6 (64) = The first read of the mate reads
Bit 7 (128) = The last read of the mate reads
Bit 8 (256) = Secondary alignment
Bit 9 (512) = Read fails quality checks
Bit 10 (1024) = Read is PCR or optical duplicate

*The value used for flag is the one specified in parenthesis in this list. Example: flag=1,8,16

Version	1.1
Bundle	sequencing
Categories
Authors	Alejandra Cervera (alejandra.cerverataboada@helsinki.fi)
Issue tracker	View/Report issues
Requires	python
Source files	component.xml flag.py
Usage	Example with default values AligFilterFlag( alignment = SAM, flag = "64" )

Inputs

Name	Type	Mandatory	Description
alignment	SAM	Mandatory	A SAM file with the alignments.

Outputs

Name	Type	Description
splitAlignments1	SAM	Alignments with the flag value.
splitAlignments2	SAM	Rest of the alignments.

Parameters

Name	Type	Default	Description
flag	string	"64"	The flag value to use for filtering, default is 64 which separates alignments based on first or second pair from a paired end read

Test cases

Test case	Parameters▼	IN alignment	OUT splitAlignments1	OUT splitAlignments2
case1	properties	alignment	(missing)	(missing)
	# Testing AligFilterFlag component, flag = 1,8,16

Generated 2019-02-08 07:42:12 by Anduril 2.0.0