fill-ref-md51
Computes md5 sum of the reference sequence
Usage
fill-ref-md5 [OPTIONS]
in.vcf.gz
out.vcf.gz
Overview
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
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-d, --dictionary <file> -
Where to read/write computed MD5s. Opened in append mode, existing records are not touched.
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-i, --info <AS:xx,SP:xx,TX:xx> -
Optional info on reference assembly (AS), species (SP), taxonomy (TX)
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-r, --refseq <file> -
The reference sequence in fasta format indexed by samtools faidx
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-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