Description Usage Arguments Value
Perform allele-specific alignment with fastq files
1 2 3 |
fastqFiles1 |
A vector of relative/absolute paths to fastq files. Each fastq file provided is parsed independently. |
fastqFiles2 |
A vector of read2 fastq files corresponding to the mate-pairs of the files defined in fastqFiles1. |
index1prefix |
A relative/absolute path to a bowtie2 index of one of the reference haplotypes. Note that the prefix of reference 1 and 2 should be different (e.g., not both be "genome") |
index2prefix |
A relative/absolute path to a bowtie2 index of the second reference haplotype. |
minAS |
An integer specifying the minimum alignment score to consider a read as aligned. |
minQual |
A positive integer specifying the nimimum alignment score to parse a read. |
threads |
A positive integer specifying the number of threads to use for alignment and parsing. |
fields |
A vector of optional sam fields to preserve in the output sam files. |
A vector of file names of the parsed sam files.
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