Casbar

SNP and methylation level calling in mapped bisulfite read data.

Web Documentation for Casbar

Input ports

1. Type: URI Object
   argument-0 [fq,fq.bgzf,fq.gz,fastq,fastq.bgzf,fastq.gz,fa,fa.bgzf,fa.gz,fasta,fasta.bgzf,fasta.gz,faa,faa.bgzf,faa.gz,ffn,ffn.bgzf,ffn.gz,fna,fna.bgzf,fna.gz,frn,frn.bgzf,frn.gz,embl,embl.bgzf,embl.gz,gbk,gbk.bgzf,gbk.gz,raw,raw.bgzf,raw.gz,sam,sam.bgzf,sam.gz,bam]
   A reference genome file. [fq,fq.bgzf,fq.gz,fastq,fastq.bgzf,fastq.gz,fa,fa.bgzf,fa.gz,fasta,fasta.bgzf,fasta.gz,faa,faa.bgzf,faa.gz,ffn,ffn.bgzf,ffn.gz,fna,fna.bgzf,fna.gz,frn,frn.bgzf,frn.gz,embl,embl.bgzf,embl.gz,gbk,gbk.bgzf,gbk.gz,raw,raw.bgzf,raw.gz,sam,sam.bgzf,sam.gz,bam]
2. Type: URI Object
   argument-1 [bam,sam,sam.bgzf,sam.gz]
   SAM input file containing four-letter read alignments (must be sorted by coordinates). [bam,sam,sam.bgzf,sam.gz]

Output ports

1. Type: URI Object
   output [vcf,vcf.bgzf,vcf.gz]
   Output file for SNPs. [vcf,vcf.bgzf,vcf.gz]
2. Type: URI Object
   bed [bed,bed.bgzf,bed.gz]
   Bed output file for methylation level calls. [bed,bed.bgzf,bed.gz]