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1 FALCO Amplicon Analysis Pipeline & Galaxy wrapper
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2 ========================================
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3
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4 FALCO variant-caller is part of the Amplicon Analysis Pipeline (AAP).
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5
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6 The typical workflow is as follows:
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7 * paired-end amplicon sequencing
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8 * merge pairs (so only overlapping pairs are included)
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9 * map the single read fastq with BWA
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10 * perform variant calling with FALCO
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11 * create (html) report of the results
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12
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13 FALCO uses samtools and straight-forward statistics to determine wether a
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14 potential variant is likely a (technical) artifact or not.
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15
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16 Input / Output
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17
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18 Input of the caller is a BAM file, output VCF
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19
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20
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21 Bug Reports & other questions
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22 =============================
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23
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24 Issues can be reported via http://www.tgac.nl/
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