Mapping and variant calling pipeline - Revision history

Moiti001: info on how to concatenate fq files

2021-11-22T11:56:38Z

info on how to concatenate fq files

← Older revision		Revision as of 13:56, 22 November 2021
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	* PREFIX - prefix for the final mapped reads file		* PREFIX - prefix for the final mapped reads file

	If you want the results to be written to this directory (not to a new directory), comment out <pre>~~READS_DIR~~: /path/to/reads/</pre>		If you want the results to be written to this directory (not to a new directory), comment out <pre>OUTDIR: /path/to/output</pre>

			For the mapping step you should have one _1 fastq file and one _2 fastq file in <code>READS_DIR</code>. If you have several _1 and _2 fastq files from the same sample, you can combine them so you have one file for all _1 reads and one for all the _2 reads. This can be done by concatenating them using <code>cat</code>, if the original files are not compressed (<code>fastq</code> or <code>fq</code> extension), or <code>zcat</code> if the original files are compressed (<code>fastq.gz</code> or <code>fq.gz</code> extension). Example where your files are in the same directory and are compressed:

			<pre>zcat *_1.fastq.gz > <new file name>_1.fastq.gz
			zcat *_2.fastq.gz > <new file name>_2.fastq.gz</pre>

	== RESULTS ==		== RESULTS ==

Moiti001: changed mapping tool

2021-11-01T09:38:22Z

changed mapping tool

← Older revision		Revision as of 11:38, 1 November 2021
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	Contact: carolina.pitabarros@wur.nl <br />		Contact: carolina.pitabarros@wur.nl <br />
	ABG<br />		ABG<br />

			Path to pipeline: /lustre/nobackup/WUR/ABGC/shared/PIPELINES/mapping-variant-calling

	[https://github.com/CarolinaPB/WUR_mapping-variant-calling Link to the repository]		[https://github.com/CarolinaPB/WUR_mapping-variant-calling Link to the repository]
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	==== Tools used: ====		==== Tools used: ====

	* Bwa - mapping		* Bwa-mem2 - mapping
	* Samtools - processing		* Samtools - processing
	* Qualimap - mapping summary		* Qualimap - mapping summary

Moiti001: added pipeline workflow, small details

2021-10-22T11:46:42Z

added pipeline workflow, small details

← Older revision		Revision as of 13:46, 22 October 2021
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	* Qualimap - mapping summary		* Qualimap - mapping summary
	* Freebayes - variant calling		* Freebayes - variant calling
			* Bcftools - VCF statistics

			{\|
			!align="center"\| [[File:mapping-variant-calling-workflow.png]]
			\|-
			\|align="center"\| ''Pipeline workflow''
			\|}

	=== Edit config.yaml with the paths to your files ===		=== Edit config.yaml with the paths to your files ===
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	* PREFIX - prefix for the final mapped reads file		* PREFIX - prefix for the final mapped reads file

	If you want the results to be written to this directory (not to a new directory), ~~open Snakefile and~~ comment out		If you want the results to be written to this directory (not to a new directory), comment out <pre>READS_DIR: /path/to/reads/</pre>

	<pre>~~workdir~~: ~~config["OUTDIR"]~~</pre>
	== RESULTS ==		== RESULTS ==

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	* '''sorted_reads''' directory with the file containing the mapped reads		* '''sorted_reads''' directory with the file containing the mapped reads
	* '''results''' directory containing the qualimap results		* '''results''' directory containing the qualimap results
	* '''variant_calling''' directory containing the variant calling VCF file		* '''variant_calling''' directory containing the variant calling VCF file and a file with with VCF statistics

Moiti001 at 14:18, 30 June 2021

2021-06-30T14:18:19Z

← Older revision		Revision as of 16:18, 30 June 2021
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	Author: Carolina Pita Barros		Author: Carolina Pita Barros <br />
	Contact: carolina.pitabarros@wur.nl		Contact: carolina.pitabarros@wur.nl <br />
	ABG		ABG<br />

	[https://github.com/CarolinaPB/WUR_mapping-variant-calling Link to the repository]		[https://github.com/CarolinaPB/WUR_mapping-variant-calling Link to the repository]

Moiti001 at 14:17, 30 June 2021

2021-06-30T14:17:06Z

← Older revision		Revision as of 16:17, 30 June 2021
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	Author: Carolina Pita Barros		Author: Carolina Pita Barros
	Contact: carolina.pitabarros@wur.nl		Contact: carolina.pitabarros@wur.nl
	ABG		ABG

Moiti001: This is a pipeline to map short reads to a reference assembly. It outputs the mapped reads, a qualimap report and does variant calling.

2021-06-30T14:16:54Z

This is a pipeline to map short reads to a reference assembly. It outputs the mapped reads, a qualimap report and does variant calling.

New page

Author: Carolina Pita Barros
Contact: carolina.pitabarros@wur.nl
ABG

[https://github.com/CarolinaPB/WUR_mapping-variant-calling Link to the repository]

== First follow the instructions here: ==

[https://carolinapb.github.io/2021-06-23-how-to-run-my-pipelines/ Step by step guide on how to use my pipelines]<br />
Click [https://github.com/CarolinaPB/snakemake-template/blob/master/Short%20introduction%20to%20Snakemake.pdf here] for an introduction to Snakemake

== ABOUT ==

This is a pipeline to map short reads to a reference assembly. It outputs the mapped reads, a qualimap report and does variant calling.

==== Tools used: ====

* Bwa - mapping
* Samtools - processing
* Qualimap - mapping summary
* Freebayes - variant calling

=== Edit config.yaml with the paths to your files ===

<pre>OUTDIR: /path/to/output
READS_DIR: /path/to/reads/ # don't add the reads files, just the directory where they are
ASSEMBLY: /path/to/assembly
PREFIX: <output name></pre>
* OUTDIR - directory where snakemake will run and where the results will be written to
* READS_DIR - path to the directory that contains the reads
* ASSEMBLY - path to the assembly file
* PREFIX - prefix for the final mapped reads file

If you want the results to be written to this directory (not to a new directory), open Snakefile and comment out

<pre>workdir: config["OUTDIR"]</pre>
== RESULTS ==

* dated file with an overview of the files used to run the pipeline (for documentation purposes)
* '''sorted_reads''' directory with the file containing the mapped reads
* '''results''' directory containing the qualimap results
* '''variant_calling''' directory containing the variant calling VCF file