Galaxy | Published Workflow | FastQ to High Quality, Filtered, Headered, Sorted BAM / UAB

Published Workflows | ozborn | FastQ to High Quality, Filtered, Headered, Sorted BAM

Galaxy Workflow ' FastQ to High Quality, Filtered, Headered, Sorted BAM'

Annotation: Improper reads discarded, focus on quality

Step	Annotation
Step 1: Map with BWA for Illumina Will you select a reference genome from your history or use a built-in index? Use a built-in index Select a reference genome hg38full Is this library mate-paired? Paired-end Forward FASTQ file select at runtime Reverse FASTQ file select at runtime BWA settings to use Full Parameter List Maximum edit distance (aln -n) 0 Fraction of missing alignments given 2% uniform base error rate (aln -n) 0.04 Maximum number of gap opens (aln -o) 1 Maximum number of gap extensions (aln -e) -1 Disallow long deletion within [value] bp towards the 3'-end (aln -d) 16 Disallow insertion/deletion within [value] bp towards the end (aln -i) 5 Number of first subsequences to take as seed (aln -l) -1 Maximum edit distance in the seed (aln -k) 2 Mismatch penalty (aln -M) 3 Gap open penalty (aln -O) 11 Gap extension penalty (aln -E) 4 Proceed with suboptimal alignments if there are no more than INT equally best hits. (aln -R) Not available. Disable iterative search (aln -N) False Maximum number of alignments to output in the XA tag for reads paired properly (samse/sampe -n) 3 Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons) (sampe -N) 10 Maximum insert size for a read pair to be considered as being mapped properly (sampe -a) 500 Maximum occurrences of a read for pairing (sampe -o) 100000 Specify the read group for this file? (samse/sampe -r) Yes Read group identiﬁer (ID). Each @RG line must have a unique ID. The value of ID is used in the RG tags of alignment records. Must be unique among all read groups in header section. Empty. Sequencing center that produced the read (CN) Empty. Description (DS) Empty. Date that run was produced (DT) Empty. Flow order (FO). The array of nucleotide bases that correspond to the nucleotides used for each ﬂow of each read. Empty. The array of nucleotide bases that correspond to the key sequence of each read (KS) Empty. Library name (LB) Empty. Programs used for processing the read group (PG) Empty. Predicted median insert size (PI) Empty. Platform/technology used to produce the reads (PL) Empty. Platform unit (PU) Empty. Sample (SM) Empty. Suppress the header in the output SAM file False
Step 2: Filter SAM Select dataset to filter Output dataset 'output' from step 1 Flags Flag 1 Type Read is mapped in a proper pair Set the states for this flag Yes Flag 2 Type The read fails platform/vendor quality checks Set the states for this flag No Flag 3 Type The read is a PCR or optical duplicate Set the states for this flag No
Step 3: Sort Sort Dataset Output dataset 'out_file1' from step 2 on column 4 with flavor Numerical sort everything in Ascending order Column selections
Step 4: SAM-to-BAM Choose the source for the reference genome Use a built-in genome SAM file to convert Output dataset 'out_file1' from step 3 Using reference genome None