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

StepAnnotation
Step 1: Map with BWA for Illumina
Use a built-in index
hg38full
Paired-end
select at runtime
select at runtime
Full Parameter List
0
0.04
1
-1
16
5
-1
2
3
11
4
Not available.
False
3
10
500
100000
Yes
Empty.
Empty.
Empty.
Empty.
Empty.
Empty.
Empty.
Empty.
Empty.
Empty.
Empty.
Empty.
False
Step 2: Filter SAM
Output dataset 'output' from step 1
Flags
Flag 1
Read is mapped in a proper pair
Yes
Flag 2
The read fails platform/vendor quality checks
No
Flag 3
The read is a PCR or optical duplicate
No
Step 3: Sort
Output dataset 'out_file1' from step 2
4
Numerical sort
Ascending order
Column selections
Step 4: SAM-to-BAM
Use a built-in genome
Output dataset 'out_file1' from step 3
None