./biology/vcf-split, Split a multi-sample VCF into single-sample VCFs

[ CVSweb ] [ Homepage ] [ RSS ] [ Required by ] [ Add to tracker ]


Branch: CURRENT, Version: 0.1.5, Package name: vcf-split-0.1.5, Maintainer: bacon

Vcf-split splits a multi-sample VCF into single-sample VCFs, writing thousands
of output files simultaneously. Parsing the TOPMed human chromosome 1 BCF
with bcftools takes two days, so extracting the 137,977 samples one at a time
or using thousands of parallel readers of the same file is impractical.
Vcf-split solves this by generating thousands of single-sample outputs during
a single sweep through the multi-sample input.


Master sites:

Filesize: 21.856 KB

Version history: (Expand)


CVS history: (Expand)


   2022-06-11 21:46:43 by Jason Bacon | Files touched by this commit (3)
Log message:
biology/vcf-split: Update to 0.1.5

Use latest biolibc API
Minor build system improvements
https://github.com/auerlab/vcf-split/releases
   2022-03-15 22:12:52 by Jason Bacon | Files touched by this commit (3) | Package updated
Log message:
biology/vcf-split: Update to 0.1.4

Minor update for biolibc 0.2.2 API changes
   2021-12-14 20:10:43 by Jason Bacon | Files touched by this commit (3)
Log message:
biology/vcf-split: Update to 0.1.3.3

Transfer header from multi-sample input
Updates for evolving libxtend and biolibc APIs
Add --version flag
Numerous minor fixes and enhancements
   2021-10-26 12:03:45 by Nia Alarie | Files touched by this commit (73)
Log message:
biology: Replace RMD160 checksums with BLAKE2s checksums

All checksums have been double-checked against existing RMD160 and
SHA512 hashes
   2021-10-07 15:19:44 by Nia Alarie | Files touched by this commit (73)
Log message:
biology: Remove SHA1 hashes for distfiles
   2021-06-11 19:22:40 by Jason Bacon | Files touched by this commit (3)
Log message:
biology/vcf-split: Update to 0.1.2

Updates for new biolibc API

Upstream change log: https://github.com/auerlab/vcf-split/releases
   2021-03-24 16:22:29 by Jason Bacon | Files touched by this commit (4)
Log message:
biology/vcf-split: import vcf-split-0.1.1

Vcf-split splits a multi-sample VCF into single-sample VCFs, writing thousands
of output files simultaneously.  Parsing the TOPMed human chromosome 1 BCF
with bcftools takes two days, so extracting the 137,977 samples one at a time
or using thousands of parallel readers of the same file is impractical.
Vcf-split solves this by generating thousands of single-sample outputs during
a single sweep through the multi-sample input.