Mercurial > repos > stef > falco
changeset 89:cf271f328d5e draft
Uploaded
| author | stef |
|---|---|
| date | Fri, 17 Jul 2015 06:02:36 -0400 |
| parents | 8aa51c577802 |
| children | 07c810e4061c |
| files | README.md README.rst falco/lib/perl/qc2vcf.pl |
| diffstat | 3 files changed, 38 insertions(+), 27 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri Jul 17 06:02:36 2015 -0400 @@ -0,0 +1,35 @@ +FALCO Galaxy tool +==================== + +This galaxy-tool is a wrapper for the Amplicon Variant Caller FALCO + +FALCO is part of the Amplicon Analysis Pipeline (AAP). + +The typical workflow is as follows: +* paired-end amplicon sequencing +* merge pairs (so only overlapping pairs are included) +* map the single read fastq with BWA +* perform variant calling with FALCO (input=BAM, output=VCF) +* create (html) report of the results + +FALCO uses samtools and straight-forward statistics to determine whether a +potential variant is likely a (technical) artifact or not. + +For questions/remarks about the underlying tool itself, see [FALCO at github]. Issues can also be reported the via [TGAC website] + +[Falco at github]: https://github.com/tgac-vumc/falco/ +[TGAC website]: http://www.tgac.nl/ + +Installation +--------------------- + +This tool should be installed into a galaxy installation from the (test)toolshed (tool-name: falco). + + +Citation +--------------------- + +For the underlying tool please cite: + +Daoud Sie, Peter J.F. Snijders, Gerrit A. Meijer, Marije W. Doeleman, Marinda I. H. van Moorsel, Hendrik F. van Essen, Paul P. Eijk, Katrien Grünberg, Nicole C. T. van Grieken, Erik Thunnissen, Henk M. Verheul, Egbert F. Smit, Bauke Ylstra, Daniëlle A. M. Heideman "Performance of amplicon-based next generation DNA sequencing for diagnostic gene mutation profiling in oncopathology" Cellular Oncology 37.5 (2014):353-361 doi:10.1007/s13402-014-0196-2 +
--- a/README.rst Thu Apr 23 10:51:43 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ -FALCO Amplicon Analysis Pipeline & Galaxy wrapper -======================================== - -FALCO variant-caller is part of the Amplicon Analysis Pipeline (AAP). - -The typical workflow is as follows: -* paired-end amplicon sequencing -* merge pairs (so only overlapping pairs are included) -* map the single read fastq with BWA -* perform variant calling with FALCO -* create (html) report of the results - -FALCO uses samtools and straight-forward statistics to determine wether a -potential variant is likely a (technical) artifact or not. - -Input / Output - -Input of the caller is a BAM file, output VCF - - -Bug Reports & other questions -============================= - -Issues can be reported via http://www.tgac.nl/
--- a/falco/lib/perl/qc2vcf.pl Thu Apr 23 10:51:43 2015 -0400 +++ b/falco/lib/perl/qc2vcf.pl Fri Jul 17 06:02:36 2015 -0400 @@ -76,7 +76,7 @@ my $gt = "$row[$ref]/$VAR"; my $qual = $row[$varQual] || 0; $skip++ if ($qual == 0); - my $filter = 0; + my $filter = '.'; my $info = "TARGET=$row[$target]"; my $format = "DP:AD:AB"; my $sample = "$row[$dp]:$row[$nref],$dpVar:$vaf"; @@ -103,7 +103,7 @@ my $gt = "$row[$ref]/$keys[0]"; my $qual = $row[$insQual]; $skip++ if ($qual == 0); - my $filter = 0; + my $filter = '.'; my $info = "TARGET=$row[$target]"; my $format = "DP:AD:AB"; my $sample = "$DP:$nREF,$nins:$vaf"; @@ -129,7 +129,7 @@ my $gt = "$keys[0]/$row[$ref]"; my $qual = $row[$delQual]; $skip++ if ($qual == 0); - my $filter = 0; + my $filter = '.'; my $info = "TARGET=$row[$target]"; my $format = "DP:AD:AB"; my $sample = "$DP:$nREF,$ndel:$vaf";