Changes between Version 6 and Version 7 of SOPs/vcf_manipulation

Timestamp:

10/07/15 14:29:10 (9 years ago)

Author:

gbell

Comment:

--

SOPs/vcf_manipulation

@@ -61 +61 @@
 }}}
 
+Annotate variants if known SNPs
+{{{
+# Index VCF file of SNPs (or other annotations)
+bgzip dbSNP.version.vcf
+tabix -p vcf dbSNP.version.vcf.gz
+# Use annotation file to add info to ID column (if there's overlap between variant and annotation)
+vcf-annotate -a dbSNP.version.vcf.gz -c CHROM,POS,ID,-,-,-,-,- -d key=INFO,ID=RS_ID,Number=1,Type=Integer,Description="SNPs from a subset of dbSNP" < My_variants.hg38.vcf > My_variants.hg38.dbSNP.vcf
+}}}
+See [http://www.htslib.org/doc/tabix.html tabix] for how to index BED or other file types.
+See [http://vcftools.sourceforge.net/perl_module.html#vcf-annotate vcf-annotate] for details of last command.
 
 Sort by chromosome and then coordinates