Tags

v1.5

version 1.5: public opening of snakealign

v1.4

version 1.4: addition of rsID and functionnal annotation

v1.3

version 1.3: run time improvment: genomicsdbimport and genotypegvcf paralellisation per chromosome

v1.2

version 1.2: imputation and phasing operated

v1.1.corrected.gatk4.2.2.0

Release version v1.1.corrected.gatk4.2.2.0 - update gatk version to 4.2.2.0 ; 2024-04-02

v1.1.corrected

this branch was used to add an offset (1kb) before and after each chunk (5Mb) created to run beagle to make correct predictions
this offset (overhang) is cut off the vcf chunk files before concatenation to one vcf file
the vcf is then cut into one file per autosome ; shapeit is run on autosomes

an addition has been made:
graphs for QD, QUAL, FS and VQSLOD have been generated before and after filtering with bcftools
a process has been added to generate these graphs with an image download of a singularity R imagecontaining necessary libraries (image made specially by Cervin)

v1.1

Release version v1.1 - 2024-01-30 - including vcf improvment: phasing and imputation (beagle, shapeit)

v1.0

Release version v1.0 - first version applied - 2023-11-13

v0.3

Release version v0.3 - addition of final_varpipeline.sh ; 2023-10-02

tag_after_multiruns

multi runs samples processing has been developped

Tag_before_multiRuns

save the work before modifications for multi runs samples processing and merging multiruns branch

v0.2

Release version v0.2 - genobioinfo cluster adaptation - step2 gatk nextflow operable - gvcf_tmp managment for variant detection part (step2) - read group syntaxe for fastq file name (ID_library.fastq.gz) ; 2023-06-12

v0.1

Release version v0.1 - fastq processing to g.vcf, and genotyping are operables

tag_2022-03-15

this tag aims at recovering the code used to produce result files and allows generating the first varpipeline release

branch1