https://github.com/brentp/tiwih - meandepth better on small chromosomes

- Nim
Published by brentp about 3 years ago

https://github.com/brentp/tiwih - meandepth per chromosome

tiwih is distributed as a static linux binary. Just download the binary below, chmod +x and run it directly. It will show a list of subcommands (also documented in the readme).

v0.1.9

• meandepth: add --chromosome(s) argument. This lets us check particular chromosomes and allows a quick sex-check. e.g. tiwih meandepth --chromosome chr1,chr2,chrX,chrY $bam will output something like: chr1 55 chr2 57 chrX 28 chrY 28

which indicates that this sample has one X and one Y chromosome.

- Nim
Published by brentp over 3 years ago

https://github.com/brentp/tiwih - vcf2bedpe: also write svtype

- Nim
Published by brentp about 4 years ago

https://github.com/brentp/tiwih -

vcf2bedpe added

- Nim
Published by brentp about 4 years ago

https://github.com/brentp/tiwih - pedbam

v0.1.6

• new tool: pedbam: adds a path column to a pedigree file given a ped file and a list of bams

- Nim
Published by brentp almost 5 years ago

https://github.com/brentp/tiwih - setsvalt changes

setsvalt also now sets the reference allele and capitalizes the ref and alt.

- Nim
Published by brentp almost 5 years ago

https://github.com/brentp/tiwih - start > 151

fixes problems with paragraph

- Nim
Published by brentp almost 5 years ago

https://github.com/brentp/tiwih - setsvalt + jasmine

v0.1.3

• svsetalt: update for jasmine peculiarities

- Nim
Published by brentp almost 5 years ago

https://github.com/brentp/tiwih - meandepth fix

v0.1.2

• meandepth: fix so that we don't need read sequence to count read-length. (just use cigar).

- Nim
Published by brentp almost 5 years ago

https://github.com/brentp/tiwih - jigv tsv

- Nim
Published by brentp almost 5 years ago

https://github.com/brentp/tiwih - bugfix

minor

- Nim
Published by brentp about 5 years ago

https://github.com/brentp/tiwih - new tool: `slivar_jigv_links`

new tool: slivar_jigv_links: add jigv links to the tsv

- Nim
Published by brentp about 5 years ago

https://github.com/brentp/tiwih - split slivar

v0.0.8

• new tool: slivar_split_fam: split joint slivar files by family and inheritance mode

- Nim
Published by brentp about 5 years ago

https://github.com/brentp/tiwih - sum_slivar_counts

v0.0.7

• new tool: sum_slivar_counts: adds the slivar variant counts in case of parallelization across regions.

- Nim
Published by brentp about 5 years ago

https://github.com/brentp/tiwih - combine_slivar_counts fixes

v0.0.6

• [combineslivarcounts]: handles cases where we got family-based counts (with zeros) in one file that are missing in the compound-het file. also allows dropping files with zero samples.

- Nim
Published by brentp about 5 years ago

https://github.com/brentp/tiwih - combine_slivar_hets

- Nim
Published by brentp about 5 years ago

https://github.com/brentp/tiwih - setsvalt

- Nim
Published by brentp about 5 years ago

https://github.com/brentp/tiwih - add fai regions

- Nim
Published by brentp about 5 years ago

https://github.com/brentp/tiwih - setref

add setref allele and make meandepth faster.

- Nim
Published by brentp about 5 years ago

https://github.com/brentp/tiwih - initial release

see static binary for linux below

- Nim
Published by brentp about 5 years ago