Michael R. Crusoe pushed to branch master at Debian Med / qtltools
Commits: 1bab2a47 by Michael R. Crusoe at 2020-10-13T15:40:32+02:00 Install the new files in appropriate locations. - - - - - 574bb232 by Michael R. Crusoe at 2020-10-13T17:56:42+02:00 release 1.3.1+dfsg-2 - - - - - 4 changed files: - − debian/QTLtools.1 - debian/changelog - debian/qtltools.install - debian/qtltools.manpages Changes: ===================================== debian/QTLtools.1 deleted ===================================== @@ -1,100 +0,0 @@ -.\" -.TH QTLtools "1" "November 2016" "1.0" -.SH NAME -QTLtools \- Tool set for molecular QTL discovery and analysis -.SH SYNOPSIS -.B QTLtools [\fImode\fR] [\fIoptions\fR] -.SH DESCRIPTION -QTLtools is a tool set for molecular QTL discovery and analysis. -It allows user to go from the raw sequence data to collection of molecular -Quantitative Trait Loci (QTLs) in few easy-to-perform steps. -.SH MODE -.TP -\fBbamstat\fR -Calculate basic QC metrics for BAM/SAM. -.br -To check the quality of some sequence data by counting the number of reads mapped to the reference genome and falling within a reference annotation. -.TP -\fBmatch\fR -Match VCF genotypes to BAM/SAM file. -.br -To ensure good match between the sequence and genotype data. -This is useful to detect sample mislabeling, contamination or PCR amplification biases. -.TP -\fBquan\fR -Quantification mode. -.br -To quantify exon and gene expression levels given a reference annotation such as GENCODE. -.TP -\fBpca\fR -Calculate principal components for a BED/VCF/BCF file. -.br -To perform Principal Component Analysis (PCA) on genotype or molecular phenotype data. -.TP -\fBcis\fR -cis QTL analysis. -.br -To map molecular Quantitative Trait Loci (mQTLs) in cis (i.e. proximal to the phenotype). -This mode extends FastQTL by including two additional options: (i) to study groups of phenotypes such as genes containing multiple exons or (ii) to perform conditional analysis in order to discover multiple mQTLs per phenotype. -.TP -\fBtrans\fR -trans QTL analysis. -.br -To map QTLs in trans. -This can be done either using a full permutation scheme or with a much quicker approximation. -.TP -\fBfdensity\fR -Functional density around QTLs. -.br -To measure the density of functional annotations around the QTL locations. -Useful to look at the degree of overlap between QTLs and functional annotations. -.TP -\fBfenrich\fR -Functional enrichment for QTLs. -.br -To measure how QTLs are enriched in any given functional annotations. -.TP -\fBrtc\fR -Regulatory Trait Concordance analysis. -.br -To co-localize collections of QTLs with collection of GWAS hits. - -.SH OPTIONS -.TP -\fB\-\-help\fR -.br -Print help about options for the selected mode. - -.SH EXAMPLE - -\fBQTLtools\fR \fBbamstat\fR --help - -\fBQTLtools\fR \fBbamstat\fR --bam HG00381.chr22.bam --bed gencode.v19.exon.chr22.bed.gz --filter-mapping-quality 150 --out HG00381.chr22.bamstat.txt -.br -\fBQTLtools\fR \fBmatch\fR --bam HG00381.chr22.bam --vcf genotypes.chr22.vcf.gz --filter-mapping-quality 150 --out HG00381.chr22.bamstat.txt -.br -\fBQTLtools\fR \fBquan\fR --bam HG00381.chr22.bam --gtf gencode.v19.annotation.chr22.gtf.gz --samples HG00381 --out-prefix HG00381 --filter-mapping-quality 150 --filter-mismatch 5 --filter-mismatch-total 5 --rpkm --no-merge -.br -\fBQTLtools\fR \fBpca\fR --bed genes.50percent.chr22.bed.gz --scale --center --out genes.50percent.chr22 -.br -\fBQTLtools\fR \fBcis\fR --vcf genotypes.chr22.vcf.gz --bed genes.50percent.chr22.bed.gz --cov genes.covariates.pc50.txt.gz --nominal 0.01 --region chr22:17000000-18000000 --out nominals.txt -.br -\fBQTLtools\fR \fBcis\fR --vcf genotypes.chr22.vcf.gz --bed genes.50percent.chr22.bed.gz --cov genes.covariates.pc50.txt.gz --permute 1000 --region chr22:17000000-18000000 --out permutations.txt -.br -\fBQTLtools\fR \fBcis\fR --vcf genotypes.chr22.vcf.gz --bed genes.50percent.chr22.bed.gz --cov genes.covariates.pc50.txt.gz --mapping permutations_all.thresholds.txt --chunk 12 16 --out conditional_12_16.txt -.br -\fBQTLtools\fR \fBtrans\fR --vcf genotypes.chr22.vcf.gz --bed genes.simulated.chr22.bed.gz --nominal --threshold 1e-5 --out trans.nominal -.br -\fBQTLtools\fR \fBtrans\fR --vcf genotypes.chr22.vcf.gz --bed genes.simulated.chr22.bed.gz --sample 1000 --normal --out trans.sample -.br -\fBQTLtools\fR \fBfdensity\fR --qtl results.genes.significant.bed --bed TFs.encode.bed.gz --out density.TF.around.QTL.txt -.br -\fBQTLtools\fR \fBfenrich\fR --qtl results.genes.significant.bed --tss results.genes.quantified.bed --bed TFs.encode.bed.gz --out enrichement.QTL.in.TF.txt -.br -\fBQTLtools\fR \fBrtc\fR --vcf genotypes.chr22.vcf.gz --bed genes.50percent.chr22.bed.gz --cov genes.covariates.pc50.txt.gz --hotspot hotspots_b37_hg19.bed --gwas-cis GWAS.b37.txt permutations_all.significant.txt --normal --out rtc_results.txt -.br - -.SH SEE ALSO -.BR https://qtltools.github.io/qtltools/ -.SH AUTHOR -QTLtools was written by Olivier Delaneau, Halit Ongen and Manolis Dermitzakis. ===================================== debian/changelog ===================================== @@ -1,3 +1,10 @@ +qtltools (1.3.1+dfsg-2) unstable; urgency=medium + + * Team upload. + * Install the new files in appropriate locations. + + -- Michael R. Crusoe <[email protected]> Tue, 13 Oct 2020 17:56:30 +0200 + qtltools (1.3.1+dfsg-1) unstable; urgency=medium * Team upload. ===================================== debian/qtltools.install ===================================== @@ -1 +1,3 @@ bin/QTLtools usr/bin/ +etc/bash_completion.d/QTLtools_bash_autocomplete.bash +usr/local/bin/* usr/bin/ ===================================== debian/qtltools.manpages ===================================== @@ -1 +1 @@ -debian/QTLtools.1 +usr/local/share/man/man1/*.1 View it on GitLab: https://salsa.debian.org/med-team/qtltools/-/compare/b25e46a3d429aaa46f3e55ed1807c159e09fbe0d...574bb2324b154ad20a47becf2a6c25087d3a8894 -- View it on GitLab: https://salsa.debian.org/med-team/qtltools/-/compare/b25e46a3d429aaa46f3e55ed1807c159e09fbe0d...574bb2324b154ad20a47becf2a6c25087d3a8894 You're receiving this email because of your account on salsa.debian.org.
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