Changes between Version 4 and Version 5 of VCFAggregateScriptManual

Timestamp:

2014-09-17T13:42:16+02:00 (11 years ago)

Author:

jvelde

Comment:

--

VCFAggregateScriptManual

@@ -10 +10 @@
 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)
@@ -28 +30 @@
 == 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
+}}}
 
 ''The option -ss  is crucial here: it removed all sample details.''
@@ -60 +66 @@
 A: The are some built-in options to help with this. For example:
 
- Prepare sample VCFs for one batch; e.g. CAR_Batch1_106Samples
- cd /Volumes/CardioKitVCFs/OriginalVCFs/CAR_Batch1_106Samples
- Fix missing '>' at the end of contig meta-data lines.
-  perl -pi -e 's/(contig=<ID=[^>\n]+)$/$1>/' CAR_*/*.vcf
- Sort, filter on 'PASS', bgzip and index with tabix (vcftools will not work on uncompressed, unindexed VCF files.)
-  for item in $(ls CAR_*/*.vcf); \
-  do echo "Processing $item..."; \
-  vcf-sort $item | vcf-annotate -H > $item\.sorted\.filtered; \
-  bgzip $item\.sorted\.filtered; \
-  tabix -p vcf $item\.sorted\.filtered\.gz; \
-  done
+Prepare sample VCFs for one batch; e.g. CAR_Batch1_106Samples
 
+{{{
+cd /Volumes/CardioKitVCFs/OriginalVCFs/CAR_Batch1_106Samples
+}}}
+
+Fix missing '>' at the end of contig meta-data lines.
+
+{{{
+perl -pi -e 's/(contig=<ID=[^>\n]+)$/$1>/' CAR_*/*.vcf
+}}}
+
+Sort, filter on 'PASS', bgzip and index with tabix (vcftools will not work on uncompressed, unindexed VCF files.)
+
+{{{
+for item in $(ls CAR_*/*.vcf); \
+do echo "Processing $item..."; \
+vcf-sort $item | vcf-annotate -H > $item\.sorted\.filtered; \
+bgzip $item\.sorted\.filtered; \
+tabix -p vcf $item\.sorted\.filtered\.gz; \
+done
+}}}