meandepth better on small chromosomes

v0.2.0

better heuristic for small chromosomes

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.

vcf2bedpe: also write svtype

v0.1.8

add svtype in final column of vcf2bedpe

v0.1.7

vcf2bedpe added

pedbam

v0.1.6

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

setsvalt changes

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

start > 151

fixes problems with paragraph

setsvalt + jasmine

v0.1.3

• svsetalt: update for jasmine peculiarities

meandepth fix

v0.1.2

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

jigv tsv

new tool: slivar_jigv_tsv

 writes an html page with a table of all variants
 where row-click loads and igv.js plots the appropirate data.