updated URLs in documentation

grunwaldlab · Aug 28, 2020 · 8d1fa3f · 8d1fa3f
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diff --git a/README.md b/README.md
@@ -129,9 +129,9 @@ If you know of a software that I have not included on this list, particularly if
 
 * [Cortex](http://cortexassembler.sourceforge.net/)
 * [freebayes](https://github.com/ekg/freebayes)
-* [GATK haplotype caller](https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php)
-* [GATK MuTect2](https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php)
-* [GATK GenotypeGVCFs](https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_variantutils_GenotypeGVCFs.php)
+* [GATK haplotype caller](https://software.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php)
+* [GATK MuTect2](https://software.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php)
+* [GATK GenotypeGVCFs](https://software.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_variantutils_GenotypeGVCFs.php)
 * [LoFreq](http://csb5.github.io/lofreq/)
 * [Samtools](http://www.htslib.org/)
 * [VarScan2](http://dkoboldt.github.io/varscan/)
@@ -140,7 +140,7 @@ If you know of a software that I have not included on this list, particularly if
 **Restriction site associated DNA markers (e.g., RADseq, GBS):**
 
 * [Stacks](http://catchenlab.life.illinois.edu/stacks/)
-* [Tassel](http://www.maizegenetics.net/#!tassel/c17q9)
+* [Tassel](https://www.maizegenetics.net)
 
 **Manipulation of VCF data:**
 

diff --git a/vignettes/intro_to_vcfR.Rmd b/vignettes/intro_to_vcfR.Rmd
@@ -41,7 +41,7 @@ This is one situation where not having complete chromosomes actually can be an a
 ## Data input
 
 
-The vcfR package is designed to work with data from [VCF](http://www.1000genomes.org/node/101) files.
+The vcfR package is designed to work with data from [VCF](https://www.internationalgenome.org/node/101) files.
 The use of a sequence file ([FASTA format](https://en.wikipedia.org/wiki/FASTA_format)) and an annotation file ([GFF format](https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md)) can provide helpful context, but are not required.
 We'll begin our example by locating the data files from the package 'pinfsc50.'