hts-specs
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samtools
Specifications of SAM/BAM and related high-throughput sequencing file formats
Brought up in the "Future of VCF" call, it was suggested to put example VCFs in this repo, but as regular files (not inside the Spec .tex) for external tools...
VCF 4.4 allows setting the first phasing indicitor in a genotype (GT) value, i.e., > The first phasing indicator may be omitted and is implicitly defined as / if any...
In VCF 4.3, the concept of structured and unstructured records was introduced, which requires all structured records to include an ID field (§ 1.4 "[Meta-information lines](https://samtools.github.io/hts-specs/VCFv4.3.pdf#subsection.1.4)" (2022-11-27)). Was this a...
Please review and provide feedback. - Rebased #434 onto VCFv4.5 - Made LAA 0-based inclusive of REF - Added FORMAT END instead of #435 Logic behind going with FORMAT END:...
This is in regard to _Sequence Alignment/Map Optional Fields Specification_ (2022-08-17). The base modifications (`MM`) field allows modifications to be either short codes or an ChEBI ID. Short codes are...
A recent GATK change replaces GT ./. due to DP=0 with 0/0 (with GQ=0). A big argument erupted on the internet regarding the "breaking of the VCF spec" I was...
It would be amazing if all of the file types specified here such as VCF v4.2 had a formally defined and [registered MIME type with the IANA](https://www.iana.org/form/media-types) for use in...
I would like to retrieve the alignment information for a given secondary or supplementary alignment . For example, in duplicate marking, we may choose to use the primary alignments of...
We already have a recommendation that MAPQ of 255 should not be used. Expand on this to recommend zero is used when unmapped. This is purely a recommendation, made for...
In [`test/vcf/4.3/passed/passed_meta_contig.vcf`](https://github.com/samtools/hts-specs/blob/7554e7c7cddacc92e2e467d6f1e0692d626752a0/test/vcf/4.3/passed/passed_meta_contig.vcf), there are two `contig` header records with the same ID. ``` ##contig= ##contig= ``` As per § 1.4 "[Meta-information lines](https://samtools.github.io/hts-specs/VCFv4.3.pdf#subsection.1.4)" (2022-11-27): > All structured lines require an ID...