fill-ref-md5 - computes MD5 sum of the reference sequence
fill-ref-md5 [OPTIONS] in.vcf.gz
out.vcf.gz
About: The script computes MD5 sum of the reference sequence and
inserts
- 'reference' and 'contig' tags into header as recommended by VCFv4.1. The
VCF file must be compressed and tabix indexed, as it takes advantage of
the lightning fast tabix reheader functionality.
- -d, --dictionary
<file>
- Where to read/write computed MD5s. Opened in append mode, existing records
are not touched.
- -i, --info
<AS:xx,SP:xx,TX:xx>
- Optional info on reference assembly (AS), species (SP), taxonomy (TX)
- -r, --refseq
<file>
- The reference sequence in fasta format indexed by samtools faidx
- -h, -?,
--help
- This help message.