fill-ref-md5 (1)

Computes md5 sum of the reference sequence

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  4. fill-ref-md5: Computes md5 sum of the reference sequence
  1. Carta.tech
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  3. vcftools
  4. fill-ref-md5: Computes md5 sum of the reference sequence

SYNOPSIS

fill-ref-md5 [OPTIONS] in.vcf.gz out.vcf.gz

DESCRIPTION

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.

OPTIONS

-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.

EXAMPLES

fill-ref-md5 -i AS:NCBIM37,SP:"Mus\ Musculus" -r NCBIM37_um.fa

-d NCBIM37_um.fa.dict in.vcf.gz out.vcf.gz