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annotate

Merge csv file with with tabix indexed file. This command could be used to annotate variants.

Index files

Downloads a csv file from pheweb resources

Mapping files from pheweb are available on: https://resources.pheweb.org/

wget https://resources.pheweb.org/rsids-v154-hg19.tsv.gz

Add header, convert to bgzip format and create index on CHROM and POS:

echo -e "CHROM\tPOS\tRSID\tREF\tALT" | bgzip -c > rsids-v154-hg19.index.gz
gzcat rsids-v154-hg19.tsv.gz | bgzip -c >> rsids-v154-hg19.index.gz
tabix -s1 -b2 -e2 -S1 rsids-v154-hg19.index.gz

Note: Replace gzcatwith zcaton linux.

Basic usage

Annotate regenie file with rsID

Annotate file regenie.txt.gz with rsID from rsids-v154-hg19.index.gz and store output in regenie.annotated.txt:

java -jar genomic-utils.jar annotate \
  --input regenie.txt.gz \
  --chr CHROM \
  --pos GENPOS \
  --ref ALLELE0 \
  --alt ALLELE1 \
  --anno rsids-v154-hg19.index.gz \
  --anno-columns RSID \
  --strategy CHROM_POS_ALLELES \
  --output regenie.annotated.txt