diff --git a/docs/pipelines/bam2wig.md b/docs/pipelines/bam2wig.md
index a5f8dc56338e2ad5da06201fde4d4f90f5fc5e3e..3900c7d8150e6610750de84f7ef573186916f435 100644
--- a/docs/pipelines/bam2wig.md
+++ b/docs/pipelines/bam2wig.md
@@ -46,3 +46,8 @@ To run the pipeline:
 ## Output Files
 
 The pipeline generates three output track files: a bigWig file, a wiggle file, and a TDF file.
+
+## Getting Help
+
+If you have any questions on running Bam2Wig or suggestions on how to improve the overall flow, feel free to post an issue to our
+ issue tracker at [GitHub](https://github.com/biopet/biopet). Or contact us directly via: [SASC email](mailto: SASC@lumc.nl)
diff --git a/docs/pipelines/basty.md b/docs/pipelines/basty.md
index 0cb4d29ae94b76c669f4bb71aa2454d82effe8c1..f053f208de334b5475f5d97576ca0d609abddf18 100644
--- a/docs/pipelines/basty.md
+++ b/docs/pipelines/basty.md
@@ -152,3 +152,8 @@ The output files this pipeline produces are:
 
 
 ## References
+
+## Getting Help
+
+If you have any questions on running Basty, suggestions on how to improve the overall flow, or requests for your favorite 
+SNP typing algorithm, feel free to post an issue to our issue tracker at [GitHub](https://github.com/biopet/biopet). Or contact us directly via: [SASC email](mailto:SASC@lumc.nl)
diff --git a/docs/pipelines/carp.md b/docs/pipelines/carp.md
index c39535f9e64a6c2f9188bc4d0f5ad3ec5894c44f..7149c1a804f51d54379898379e2014003762f207 100644
--- a/docs/pipelines/carp.md
+++ b/docs/pipelines/carp.md
@@ -209,6 +209,6 @@ with your pipeline runs.
 
 ## Getting Help
 
-If you have any questions on running Carp, suggestions on how to improve the overall flow, or requests for your favorite ChIP-seq related program to be added, feel free to post an issue to our issue tracker at [https://git.lumc.nl/biopet/biopet/issues](https://git.lumc.nl/biopet/biopet/issues).
-Or contact us directly via: [SASC email](mailto: SASC@lumc.nl)
+If you have any questions on running Carp, suggestions on how to improve the overall flow, or requests for your favorite ChIP-seq related program to be added, feel free to post an issue to our issue tracker at [GitHub](https://github.com/biopet/biopet).
+Or contact us directly via: [SASC email](mailto:SASC@lumc.nl)
 
diff --git a/docs/pipelines/flexiprep.md b/docs/pipelines/flexiprep.md
index c47732029701c3bd26278e85c4ce32327361f879..e39755d6eb5e0067e5fe146906ecea2188306778 100644
--- a/docs/pipelines/flexiprep.md
+++ b/docs/pipelines/flexiprep.md
@@ -145,3 +145,9 @@ The pipeline also outputs 2 Fastqc runs one before and one after quality control
 └── report
 
 ~~~
+
+## Getting Help
+
+If you have any questions on running Flexiprep, suggestions on how to improve the overall flow, or requests for your favorite 
+Quality Control (QC) related program to be added, feel free to post an issue to our issue tracker at [GitHub](https://github.com/biopet/biopet).
+Or contact us directly via: [SASC email](mailto:SASC@lumc.nl)
diff --git a/docs/pipelines/gentrap.md b/docs/pipelines/gentrap.md
index 9cbe719e92d37fdb5a46c3f24ac3c0da326be173..e7e960168facf157e654652386dbf69da073b252 100644
--- a/docs/pipelines/gentrap.md
+++ b/docs/pipelines/gentrap.md
@@ -26,7 +26,7 @@ As with other biopet pipelines, Gentrap relies on a JSON configuration file to r
 
 Samples are single experimental units whose expression you want to measure. They usually consist of a single sequencing library, but in some cases (for example when the experiment demands each sample have a minimum library depth) a single sample may contain multiple sequencing libraries as well. All this is can be configured using the correct JSON nesting, with the following pattern:
 
-~~~
+~~~ json
 {
   "samples": {
     "sample_A": {
@@ -43,7 +43,7 @@ Samples are single experimental units whose expression you want to measure. They
 
 In the example above, there is one sample (named `sample_A`) which contains one sequencing library (named `lib_01`). The library itself is paired end, with both `R1` and `R2` pointing to the location of the files in the file system. A more complicated example is the following:
 
-~~~
+~~~ json
 {
   "samples": {
     "sample_X": {
@@ -95,7 +95,7 @@ In addition to these, you must also remember to supply the alignment index requi
 
 Thus, an example settings configuration is as follows:
 
-~~~
+~~~ json
 {
   "output_dir": "/path/to/output/dir",
   "expression_measures": ["fragments_per_gene", "bases_per_gene"],
@@ -118,13 +118,13 @@ In most cases, it's practical to combine the samples and settings configuration
 
 As with other pipelines in the Biopet suite, Gentrap can be run by specifying the pipeline after the `pipeline` subcommand:
 
-~~~
+~~~ bash
 $ java -jar </path/to/biopet.jar> pipeline gentrap -config </path/to/config.json> -qsub -jobParaEnv BWA -run
 ~~~
 
 You can also use the `biopet` environment module (recommended) when you are running the pipeline in SHARK:
 
-~~~
+~~~ bash
 $ module load biopet/v0.5.0
 $ biopet pipeline gentrap -config </path/to/config.json> -qsub -jobParaEnv BWA -run
 ~~~
@@ -137,5 +137,5 @@ The number and types of output files depend on your run configuration. What you
 
 ## Getting Help
 
-If you have any questions on running Gentrap, suggestions on how to improve the overall flow, or requests for your favorite RNA-seq related program to be added, feel free to post an issue to our issue tracker at [https://git.lumc.nl/biopet/biopet/issues](https://git.lumc.nl/biopet/biopet/issues).
-
+If you have any questions on running Gentrap, suggestions on how to improve the overall flow, or requests for your favorite RNA-seq related program to be added,
+ feel free to post an issue to our issue tracker at [GitHub](https://github.com/biopet/biopet). Or contact us directly via: [SASC email](mailto:SASC@lumc.nl)
\ No newline at end of file
diff --git a/docs/pipelines/mapping.md b/docs/pipelines/mapping.md
index 0e20aeecce28fe660b6df4ebd8b05a49cf50fc13..f358eac704b4bfb42132af8e23b9a1b93ba05e73 100644
--- a/docs/pipelines/mapping.md
+++ b/docs/pipelines/mapping.md
@@ -126,3 +126,9 @@ To perform a dry run simply remove `-run` from the commandline call.
     ├── metrics
     └── report
 ~~~
+
+## Getting Help
+
+If you have any questions on running Mapping, suggestions on how to improve the overall flow, or requests for your favorite aligner to be added, feel free to post an issue to our issue tracker at
+ [GitHub](https://github.com/biopet/biopet). Or contact us directly via: [SASC email](mailto:SASC@lumc.nl)
+
diff --git a/docs/pipelines/sage.md b/docs/pipelines/sage.md
index cc62920e7c5132cabf1688a2bd83b90a95435a15..1330625e48b770a7fe08fdbcc3dae0d6bb5f0d83 100644
--- a/docs/pipelines/sage.md
+++ b/docs/pipelines/sage.md
@@ -123,3 +123,8 @@ Below is an example of the output files that you will get after running Sage. He
     ├── no_sense_genes.txt
     └── tag.lib
 ~~~
+
+## Getting Help
+
+If you have any questions on running SAGE or suggestions on how to improve the overall flow, feel free to post an issue to our issue tracker at [GitHub](https://github.com/biopet/biopet).
+Or contact us directly via: [SASC email](mailto:SASC@lumc.nl)
diff --git a/docs/pipelines/shiva.md b/docs/pipelines/shiva.md
index e0e98f4ea61c21b65b5ba2b0dc9ac9c69201e6b7..a6c9ec230c7d270fcfeda06fc0dd76816c0d49cb 100644
--- a/docs/pipelines/shiva.md
+++ b/docs/pipelines/shiva.md
@@ -174,3 +174,11 @@ The config for these therefore is:
 ```
 
 ## References
+
+* Shiva follows the best practices of GATK: [GATK best practices](https://www.broadinstitute.org/gatk/guide/best-practices)
+
+
+## Getting Help
+
+If you have any questions on running Shiva, suggestions on how to improve the overall flow, or requests for your favorite variant calling related program to be added, feel free to post an issue to our issue tracker at [GitHub](https://github.com/biopet/biopet).
+Or contact us directly via: [SASC email](mailto:SASC@lumc.nl)
diff --git a/docs/pipelines/toucan.md b/docs/pipelines/toucan.md
index 4abe874d20abd1bb875268a175f0ad93fd9cc1ae..55db00471bf693de38ffa5a41b40644377af67c6 100644
--- a/docs/pipelines/toucan.md
+++ b/docs/pipelines/toucan.md
@@ -11,6 +11,7 @@ Currently, it comprises just two steps:
 
 Example
 -----------
+
 ~~~~bash
 biopet pipeline Toucan -h
 Arguments for Toucan:
@@ -36,7 +37,8 @@ Furthermore, the `fork` field will be overwritten by `threads` in case that one
 Therefore, it is recommended not to use `fork`, but to rather use `threads`. 
 
 With that in mind, an example configuration using mode `standard` of the VepNormalizer would thus be:
-~~~~
+
+~~~ json
 {
     "varianteffectpredictor": {
         "vep_script": <path_to_exe>,
@@ -49,16 +51,24 @@ With that in mind, an example configuration using mode `standard` of the VepNorm
     },
     "output_dir": <path_to_output_directory>
 }
-~~~~
+~~~
 
 Running the pipeline
 ---------------
 The command to run the pipeline is:
-~~~~
+
+~~~~ bash
 java -jar pipeline Toucan -Input <input_vcf> -config <config_json> -run
 ~~~~
 
-If one wishes to run it on a cluster, the command becomes
-~~~~
+If one wishes to run it on a cluster, the command becomes:
+
+~~~~ bash
 java -jar pipeline Toucan -Input <input_vcf> -config <config_json> -run -qsub -jobParaEnv <PE>
 ~~~~
+
+
+## Getting Help
+
+If you have any questions on running Toucan, suggestions on how to improve the overall flow, or requests for your favorite VCF annotator to be added, feel free to post an issue to our issue tracker at [GitHub](https://github.com/biopet/biopet).
+Or contact us directly via: [SASC email](mailto:SASC@lumc.nl)
\ No newline at end of file
diff --git a/docs/tools/MpileupToVcf.md b/docs/tools/MpileupToVcf.md
index 2261e47f7a31545e681aef1a4e4d90555ba50322..f8a773ebec214a66a06951006f8fae4aad9acd7d 100644
--- a/docs/tools/MpileupToVcf.md
+++ b/docs/tools/MpileupToVcf.md
@@ -10,13 +10,13 @@ so usually one does not want to safe these files.
 
 ## Example
 To start the tool:
-~~~
+~~~ bash
 java -jar Biopet-0.2.0.jar tool mpileupToVcf
 ~~~
 
 
 To open the help:
-~~~bash
+~~~ bash
 java -jar Biopet-0.2.0.jar tool mpileupToVcf -h
 Usage: MpileupToVcf [options]
 
diff --git a/docs/tools/SamplesTsvToJson.md b/docs/tools/SamplesTsvToJson.md
index 84a33413e9d98bd110d02952aaa46a4891cf59e1..6466d484cb36abb5f7e482fcbc93ca9b21236fa4 100644
--- a/docs/tools/SamplesTsvToJson.md
+++ b/docs/tools/SamplesTsvToJson.md
@@ -3,13 +3,13 @@
 This tool enables a user to create a full sample sheet in JSON format suitable for all our Queue pipelines.
 The tool can be started as follows:
 
-~~~
+~~~ bash
 java -jar <Biopet.jar> tool SamplesTsvToJson
 ~~~
 
 To open the help:
 
-~~~
+~~~ bash
 java -jar Biopet-0.2.0.jar tool SamplesTsvToJson -h
 Usage: SamplesTsvToJson [options]
 
@@ -29,7 +29,7 @@ JSON file is parsed with those properties inside it as well. The order of column
 
 #### Example
 
-~~~
+~~~ json
 {
   "samples" : {
     "Sample_ID_1" : {
diff --git a/docs/tools/VcfFilter.md b/docs/tools/VcfFilter.md
index b9b88c9cca25f929889681317dcfcbe653dd581d..be619eee52c457a8c8e648f205e3d2c122e10caf 100644
--- a/docs/tools/VcfFilter.md
+++ b/docs/tools/VcfFilter.md
@@ -7,7 +7,8 @@ There is a wide set of options which one can use to change the filter settings.
 
 ## Example
 To open the help menu:
-~~~
+
+~~~ bash
 java -jar Biopet-0.2.0.jar tool VcfFilter -h
 Usage: VcfFilter [options]
 
@@ -47,7 +48,7 @@ Usage: VcfFilter [options]
 ~~~
 
 To run the tool:
-~~~
+~~~ bash
 java -jar Biopet-0.2.0.jar tool VcfFilter --inputVcf myInput.vcf \
 --outputVcf myOutput.vcf --filterRefCalls --minSampleDepth 
 ~~~
diff --git a/docs/tools/VcfToTsv.md b/docs/tools/VcfToTsv.md
index 4f1e294f976a97e564dbf7ec3b516271d1c153d3..31c501e5a93e0740fe549e8132dbafaa47bd50b9 100644
--- a/docs/tools/VcfToTsv.md
+++ b/docs/tools/VcfToTsv.md
@@ -8,7 +8,8 @@ There is also a possibility to only select some specific fields from you vcf and
 
 ## Example
 To open the help menu:
-~~~
+
+~~~ bash
 java -jar Biopet-0.2.0.jar tool VcfToTsv -h
 Usage: VcfToTsv [options]
 
@@ -36,7 +37,8 @@ Usage: VcfToTsv [options]
 ~~~
 
 To run the tool:
-~~~
+
+~~~ bash
 java -jar Biopet-0.2.0.jar tool VcfToTsv --inputFile myVCF.vcf \
 --outputFile my_tabDelimited_VCF.tsv --all_info
 ~~~
diff --git a/docs/tools/VepNormalizer.md b/docs/tools/VepNormalizer.md
index b361306c2c9c3986fb846903283146d0bffc1584..16f4cc4ff729e505686e4b1ec91a985c79ac4232 100644
--- a/docs/tools/VepNormalizer.md
+++ b/docs/tools/VepNormalizer.md
@@ -21,7 +21,7 @@ The CSQ tag is by default removed from the output VCF file. If one wishes to ret
 Example
 ---------
 
-~~~~bash
+~~~ bash
 biopet tool VepNormalizer -h
 |VepNormalizer - Parse VEP-annotated VCF to standard VCF format 
 Usage: VepNormalizer [options]
@@ -40,5 +40,5 @@ Usage: VepNormalizer [options]
         Mode
   --do-not-remove
         Do not remove CSQ tag
-~~~~   
+~~~   
 
diff --git a/docs/tools/WipeReads.md b/docs/tools/WipeReads.md
index 96377a03122808519293fb8204dd4144de974b1c..8aa286d93a99d1c73d8b45674e23097245ec8622 100644
--- a/docs/tools/WipeReads.md
+++ b/docs/tools/WipeReads.md
@@ -8,7 +8,8 @@ to known ribosomal RNA regions (using a supplied BED file containing intervals f
 
 ## Example
 To open the help menu:
-~~~
+
+~~~ bash
 java -jar Biopet-0.2.0.jar tool WipeReads -h
 
 WipeReads - Region-based reads removal from an indexed BAM file
@@ -54,7 +55,8 @@ the given ones, they will also be removed.
 ~~~
 
 To run the tool:
-~~~
+
+~~~ bash
 java -jar Biopet-0.2.0.jar tool WipeReads --input_file myBam.bam \
 --interval_file myRibosomal_regions.bed --output_file myFilteredBam.bam
 ~~~
diff --git a/docs/tools/sagetools.md b/docs/tools/sagetools.md
index 62451c70cc2d787c679b0ee23d3ee88296f8d7dd..8476a15c2207a556c1402f3b5b5740b9f70e1609 100644
--- a/docs/tools/sagetools.md
+++ b/docs/tools/sagetools.md
@@ -4,7 +4,8 @@ Note that these tools are already implemented in the pipeline.
 
 ## SageCountFastq
 To open the help menu:
-~~~
+
+~~~ bash
 java -jar Biopet-0.2.0.jar tool SageCreateLibrary -h
 Usage: SageCountFastq [options]
 
@@ -21,7 +22,8 @@ Usage: SageCountFastq [options]
 
 ## SageCreateLibrary
 To open the help menu:
-~~~
+
+~~~ bash
 java -jar Biopet-0.2.0.jar tool SageCreateLibrary -h
 Usage: SageCreateLibrary [options]
 
@@ -48,7 +50,8 @@ Usage: SageCreateLibrary [options]
 
 ## SageCreateTagCounts
 To open the help menu:
-~~~
+
+~~~ bash
 java -jar Biopet-0.2.0.jar tool SageCreateTagCounts -h
 Usage: SageCreateTagCounts [options]