Changes between Version 2 and Version 3 of VCFAggregateScriptManual

Timestamp:

2014-09-16T20:04:07+02:00 (10 years ago)

Author:

jvelde

Comment:

--

VCFAggregateScriptManual

@@ -33 +33 @@
 vcf-fill-gtc.pl -vcfi merged.vcf.gz -vcfo stripped.vcf -ss -fv PASS -si -ll INFO > stripped.vcf.log
 
-Super important:
-#  -ss       : remove sample details!
+''The option -ss  is crucial here: it removed all sample details.''
+
+Afterwards, be sure to inspect the log file for warnings!
+
+more stripped.vcf.log
+
+Full manual:
+
+Create a summary VCF per batch:
+ -ss       : remove sample details!
+ -fv PASS  : keep only high quality variant calls that pass all filters applied in NextGene.
+             Just to be sure: variants should already have been filtered on PASS only in a previous step,
+             so this should be redundant here...
+ -si       : remove all INFO subfields except for INFO:AN and INFO:AC.
+             INFO:AN and INFO:AC were automatically updated by vcf-merge,
+             but the others were not and may contain erroneous annotation
+             that cause vcf-validator to complain the created VCF is not valid.
+ -ll       : specifies log level, e.g. INFO
 
 
 
+== Troubleshooting ==
 
-#
-# Add bgzip and tabix to your environment.
-#
-export PATH=/Volumes/Users/Software/vcftools_0.1.10/bin/:/Volumes/Users/Software/tabix-0.2.6/:${PATH}
+Q: My VCF files are not completely valid format!
+A: The are some built-in options to help with this. For example:
 
-== Troubleshooting ==
-#
-# 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
 
-#
-# Merge sample VCFs into one batch VCF.
-#
-vcf-merge CAR_*/*.vcf.sorted.filtered.gz | bgzip -c > merged.vcf.gz
-
-#
-# Create a summary VCF per batch:
-#  -ss       : remove sample details!
-#  -fv PASS  : keep only high quality variant calls that pass all filters applied in NextGene.
-#              Just to be sure: variants should already have been filtered on PASS only in a previous step,
-#              so this should be redundant here...
-#  -si       : remove all INFO subfields except for INFO:AN and INFO:AC.
-#              INFO:AN and INFO:AC were automatically updated by vcf-merge,
-#              but the others were not and may contain erroneous annotation
-#              that cause vcf-validator to complain the created VCF is not valid.
-#
-~pneerincx/EclipseWorkspace/ngs_scripts/vcf-fill-gtc.pl -vcfi merged.vcf.gz -vcfo stripped.vcf -ss -fv PASS -si -ll INFO > stripped.vcf.log
-mv stripped.vcf      ../CAR_Batch1_106Samples.vcf
-mv stripped.vcf.log  ../CAR_Batch1_106Samples.vcf.log