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author stef
date Tue, 23 Dec 2014 11:26:33 -0500
parents 90badfe82b95
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38:f1b32c09deaf 39:a793ffd0cd04
1 Falco Amplicon Analysis Pipeline & Galaxy wrapper 1 FALCO Amplicon Analysis Pipeline & Galaxy wrapper
2 ======================================== 2 ========================================
3 3
4 Text 4 FALCO variant-caller is part of the Amplicon Analysis Pipeline (AAP).
5
6 The typical workflow is as follows:
7 * paired-end amplicon sequencing
8 * merge pairs by overlapping them
9 * map the single read fastq with BWA
10 * perform variant calling with FALCO
11 * create (html) report of the results
12
13 FALCO uses samtools and straight-forward statistics to determine wether a
14 potential variant is likely a (technical) artifact or not.
15
16 Input / Output
17 =======
18
19 Input of the caller is a BAM file, output VCF
5 20
6 21
7 History 22 History
8 ======= 23 =======
9 24
10 ============== ======================================================================== 25 ============== ================================================================
11 Date Changes 26 Date Changes
12 -------------- ------------------------------------------------------------------------ 27 -------------- ----------------------------------------------------------------
13 September 2014 * first release in Tool Shed 28 December 2014 * first release in Test Tool Shed
14 July 2014 * first release in Test Tool Shed 29 ============== ================================================================
15 ============== ========================================================================
16 30
17 31
18 Bug Reports & other questions 32 Bug Reports & other questions
19 ============================= 33 =============================
20 34
21 Issues can be reported via the contact form at 35 Issues can be reported via http://www.tgac.nl/