Shayan Doust pushed to branch master at Debian Med / marginphase
Commits: 49e3cff9 by Shayan Doust at 2020-07-01T18:19:52+01:00 Fix marginPhase.1 and write new vcfCompare.1 - - - - - 2 changed files: - debian/mans/marginPhase.1 - + debian/mans/vcfCompare.1 Changes: ===================================== debian/mans/marginPhase.1 ===================================== @@ -1,7 +1,7 @@ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15. -.TH USAGE: "1" "June 2020" "usage: marginPhase <BAM> <REFERENCE_FASTA> <PARAMS> [options]" "User Commands" +.TH MARGINPHASE "1" "June 2020" "marginPhase" "User Commands" .SH NAME -usage: \- Simultaneous haplotyping and genotyping +marginPhase \- Simultaneous haplotyping and genotyping .SH DESCRIPTION usage: marginPhase <BAM> <REFERENCE_FASTA> <PARAMS> [options] Version: 1.0.0 @@ -103,13 +103,13 @@ so reads that aren't in SNP dir are discarded example: 0 \-> N/A; 2 \-> LFP; 7 \-> LTP,LFP,LFN) .SH "SEE ALSO" The full documentation for -.B usage: +.B marginPhase is maintained as a Texinfo manual. If the .B info and -.B usage: +.B marginPhase programs are properly installed at your site, the command .IP -.B info usage: +.B info marginPhase .PP should give you access to the complete manual. ===================================== debian/mans/vcfCompare.1 ===================================== @@ -0,0 +1,23 @@ +.\" Text automatically generated by txt2man and modified by hand +.TH VCFCOMPARE "01 July 2020" "vcfCompare" "User Commands" +.SH NAME +vcfCompare \- Compares VCF_EVALUATED to VCF_REFERENCE +.SH SYNOPSIS +.B vcfCompare +[options] \fB-r\fP \fI\,VCF_REFERENCE\/\fR \fB-e\fP \fI\,VCF_EVALUATED\/\fR + +\fB-h\fP \fB--help\fP : Print this help screen + +\fB-a\fP \fB--logLevel\fP : Set the log level + +\fB-r\fP \fB--vcfReference\fP : Specify reference VCF + +\fB-e\fP \fB--vcfEvaluated\fP : Specify evaluated VCF +.SH DESCRIPTION +Compares VCF_REFERENCE to VCF_REFERENCE using the following metrics: +.IP 1. 4 +The concordance of all calls in VCF_REFERENCE compared to VCF_EVALUATED +.IP 2. 4 +The concordance of all reference positions in VCF_REFERENCE compared to VCF_EVALUATED +.IP 3. 4 +The phasing in VCF_REFERENCE compared to VCF_EVALUATED View it on GitLab: https://salsa.debian.org/med-team/marginphase/-/commit/49e3cff9a7fd895c1d5274527d2d4316396ee2b9 -- View it on GitLab: https://salsa.debian.org/med-team/marginphase/-/commit/49e3cff9a7fd895c1d5274527d2d4316396ee2b9 You're receiving this email because of your account on salsa.debian.org.
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