fill-ref-md5(1)
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
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'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>
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Where to read/write computed MD5s. Opened in append mode, existing records are not touched.
- -i, --info <AS:xx,SP:xx,TX:xx>
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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
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-d NCBIM37_um.fa.dict in.vcf.gz out.vcf.gz
-