This program examines a BAM or SAM stream (or file) for reads that contain multiple nonconverted Cs in non-CpG context. It markes these reads with a tag (XX:Z:UC) and optionally sets the vendor failed bit to prevent these reads from being used in downstream methylation calling. It also prints a count of nonconverted reads per contig to stderr.
By default, the program will read from stdin, tag reads that have 3 or more nonconverted Cs, flag them, and output to STDOUT. These can all be changed with command line arguments.
Note: This does not take read pairing into account. Each read will be tagged or not independently of its mate.
Optional arguments:
Argument
Details
–reference <Filename>
Reference fasta file [default = searches the bam file for a bwameth command]
–bam <Input file>
File must end in .bam or .sam [default = stdin]
–out <Output name>
Name of the output sam file [default = stdout]
–c_count <int>
Minimum number of nonconverted Cs on a read to consider it nonconverted [default = 3]
–flag_reads
Set the ‘Failing platform / vendor quality check’ flag [default = don’t set it]
mark-nonconverted-reads
This program examines a BAM or SAM stream (or file) for reads that contain multiple nonconverted Cs in non-CpG context. It markes these reads with a tag (XX:Z:UC) and optionally sets the vendor failed bit to prevent these reads from being used in downstream methylation calling. It also prints a count of nonconverted reads per contig to stderr.
By default, the program will read from stdin, tag reads that have 3 or more nonconverted Cs, flag them, and output to STDOUT. These can all be changed with command line arguments.
Note: This does not take read pairing into account. Each read will be tagged or not independently of its mate.
Optional arguments: