X-WGBS fill-in filtering

X-WGBS protocol for whole genome bisulfite sequencing on the Illumina X platform. Two versions of the filter script are included, filterFillIn2.pl serially processes each line of the BAM. filterFillIn3.pl chunks the BAM and processes the chunks in parallel.

Dependencies

Software/Perl Module
samtools v1.7
Bio::DB::Bam::Alignment
Getopt::Long
IPC::Cmd qw(can_run)
List::Util qw(min max)
Parallel::ForkManager
Fcntl qw(:flock SEEK_END)

Usage:

/filterFillIn(2|3).pl -b <BAM> -r <REF FASTA> -c <CHROMS>
		          -b  BAM alignment
	                  -r  Reference FASTA
                          -p  Output prefix [Default: trims *.bam]
                          -k  Keep CHH state strings [Outputs to <PREFIX>.chhStates.txt
                          -d  Fill-in distance [Default: 11bp]
[filterFillIn3.pl]        -n  Number of cores [Default: 1]
[filterFillIn3.pl]        -c  Number of lines to chunk to cores [Default: 1e5]
                          -v  Verbose mode
		          -h  Print this message

Flag	Description
-b	BAM alignment file produced by BWA-meth
-r	Indexed reference FASTA file used for alignment
-p	Output prefix. By default, replaces the *.bam extension with *.filterFillIn, and produces output *.filterFillIn.(bam|stats)
-k	Keep CHH state strings. Creates a file, PREFIX.chhStates.txt, describing the sequence of CHH calls per read with a | marking the fill-in distance position`
-d	Fill-in distance of end repair following transposition--default is 11bp
-v	Verbose mode
-h	Print a help message

Example

./filterFillIn2.pl -b test/na12878_10k_chr1.bam -r hg19.fa -p test/na12878_10k_chr1.filterFillIn -k -v
./filterFillIn3.pl -b test/na12878_10k_chr1.bam -r hg19.fa -p test/na12878_10k_chr1.filterFillIn -k -n 2 -c 1000 -v