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Use when VCF headers need reference and contig tags with MD5 checksums per VCFv4.1 specification.
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| name | fill-ref-md5 |
| description | Use when VCF headers need reference and contig tags with MD5 checksums per VCFv4.1 specification. |
| disable-model-invocation | true |
| user-invocable | true |
fill-ref-md5 [OPTIONS] in.vcf.gz out.vcf.gz/home/vimalinx/miniforge3/envs/bio/bin/fill-ref-md5references/help.md for full options and examplesreference and contig header lines with MD5 checksums to a compressed VCF.# 1) Compute MD5s from a reference FASTA and cache them in a dictionary
fill-ref-md5 -r ref.fa -d ref.fa.dict in.vcf.gz out.vcf.gz
# 2) Add assembly/species/taxonomy annotations to contig header lines
fill-ref-md5 \
-r ref.fa \
-d ref.fa.dict \
-i AS:GRCh38,SP:"Homo sapiens",TX:9606 \
in.vcf.gz out.vcf.gz
samtools faidxfill-ref-md5 -r ref.fa -d ref.fa.dict in.vcf.gz out.vcf.gz-d or -r; -d alone only works if the dictionary already contains all required chromosomes.--help works, but --version is not implemented and errors as an unknown parameter.tabix, samtools faidx, and md5sum, so those helpers must be available.