Changes between Version 1 and Version 2 of VCFAggregateScriptManual

Timestamp:

2014-09-16T19:49:43+02:00 (10 years ago)

Author:

jvelde

Comment:

--

VCFAggregateScriptManual

@@ -1 @@
-Placeholder
+= Running the VCF aggregration and de-sampling procedure =
 
-http://sourceforge.net/projects/samtools/files/tabix/
-http://vcftools.sourceforge.net/
+== 1. Install VCFtools and Tabix ==
+
+Download and install from: http://sourceforge.net/projects/samtools/files/tabix/ and http://vcftools.sourceforge.net/
+Tabix needs to be compiled first. (use MAKE )
+
+== 2. Add location of VCFtools and Tabix to your path ==
+
+E.g. use
+
+export PATH=/Volumes/Users/Software/vcftools_0.1.10/bin/:/Volumes/Users/Software/tabix-0.2.6/:${PATH}
+
+Or a more permanent option (.bashrc file or so)
+
+== 3. Download and install Perl if you don't have it ==
+
+Go to: https://www.perl.org/
+
+== 4. Download the script and put in folder of choosing ==
 
 https://github.com/molgenis/ngs-utils/blob/master/scripts/vcf-fill-gtc.pl
+
+
+= Aggregation procedure =
+
+== 1. Merge sample VCFs into one batch VCF ==
+
+vcf-merge CAR_*/*.vcf.sorted.filtered.gz | bgzip -c > merged.vcf.gz
+
+== 2. Create a summary VCF per batch ==
+
+vcf-fill-gtc.pl -vcfi merged.vcf.gz -vcfo stripped.vcf -ss -fv PASS -si -ll INFO > stripped.vcf.log
 
 Super important:
@@ -17 +44 @@
 export PATH=/Volumes/Users/Software/vcftools_0.1.10/bin/:/Volumes/Users/Software/tabix-0.2.6/:${PATH}
 
+== Troubleshooting ==
 #
 # Prepare sample VCFs for one batch; e.g. CAR_Batch1_106Samples