# HG changeset patch # User stef # Date 1419948416 18000 # Node ID 861c2e45d7c968945121acf28b4fcc7e581bf488 Uploaded diff -r 000000000000 -r 861c2e45d7c9 falco-call.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco-call.xml Tue Dec 30 09:06:56 2014 -0500 @@ -0,0 +1,131 @@ + + + + + samtools + R + + + + + + FALCO: Amplicon Analysis Pipeline + + + falco-call.sh $falco_cfg; + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \S+ + + + + + + + + + + + + + + + + + + filter_file=$filter_file + manifest_file=$manifest_file + bam_file=$bam + bam_name=$bam.name + html_out=$html_output + vcf_out=$vcf_output + out_path=${html_output.files_path} + ## reference source + REF_SOURCE="${genomeSource.refGenomeSource}" + #if $genomeSource.refGenomeSource == "history": + ##build index on the fly + REF_FILE="${genomeSource.ownFile}" + DB_KEY="${dbkey}" + #else: + ##use precomputed indexes + REF_FILE="${genomeSource.indices.fields.path}" + #end if + + + + + + + + + + + + + + + + + + +.. class:: infomark + +**Introduction** + +This tool is a wrapper for the variant caller FALCO_ which is part of the Amplicon Analysis Pipeline (AAP) + +.. _FALCO: https://github.com/tgac-vumc/falco/ + +Calls and annotates genomic variants for each amplicon in a design. + +**Notes** + +Because each amplicon is considered separate test, if two amplicons overlap this can cause the same variant position to be present twice in the output VCF. This is intentional, you can use this to evaluate the quality of the variant call beyond the amplicon. + +----- + +**Citation** + +For the underlying tool please cite: Daoud Sie et al. Performance of amplicon-based next generation DNA sequencing for diagnostic gene mutation profiling in oncopathology (Cell Oncol 2014 Oct;37(5):353-61). [Pubmed] + +.. _Pubmed: http://www.ncbi.nlm.nih.gov/pubmed/25209392 + + + +