Commit a641f0b6 authored by Gerald Salin's avatar Gerald Salin
Browse files

add max_insert_size argument

parent d87568eb
......@@ -73,6 +73,11 @@ = Sets the number of mismatches to allowed in a seed ali
alignment_mismatch.default = 1
alignment_mismatch.type = int = max_insert_size
max_insert_size.flag = --max_insert_size = The maximum insert size for valid paired-end alignments.
max_insert_size.default = 500 = bowtie2
bowtie2.flag = --bowtie2 = Use bowtie2 instead of bowtie1 (longer)
......@@ -100,4 +105,15 @@ = keep_reads
keep_reads.flag = --keep = Keep reads which pass the Illumina filters or keep reads which not pass the Illumina filters (pass_illumina_filters|not_pass_illumina_filters|all). With other values that "all" the headers of reads must be '@<instrument>:<run number>:<flowcell ID>:<lane>:<tile>:<x-pos>:<y-pos> <read>:<is filtered>:<control number>:<index sequence>'
keep_reads.default = pass_illumina_filters
keep_reads.choices = pass_illumina_filters|not_pass_illumina_filters|all
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keep_reads.choices = pass_illumina_filters|not_pass_illumina_filters|all = histogram_width
histogram_width.flag = --histogram_width = Explicitly sets the histogram width, overriding automatic truncation of histogram tail.
histogram_width.default = 500 = min_pct
min_pct.flag = --min_pct = When generating the histogram, discard any data categories (out of FR, TANDEM, RF) that have fewer than this percentage of overall reads.
min_pct.default = 0.01
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