package bamtofastq from biobambam2
https://github.com/gt1/biobambam2

package snpEff
https://salsa.debian.org/med-team/snpeff/blob/master/debian/changelog

package atropos
https://github.com/jdidion/atropos

package umis
https://github.com/vals/umis

package mosdepth
https://github.com/brentp/mosdepth

package qsignature
https://sourceforge.net/p/adamajava/wiki/Home/
https://sourceforge.net/p/adamajava/wiki/qSignature/
http://sourceforge.net/projects/adamajava/files/qsignature.tar.bz2/download
https://sourceforge.net/p/adamajava/code/HEAD/tree/trunk/adamajava/qsignature/

package optitype
https://github.com/FRED-2/OptiType

package vcfanno
https://github.com/brentp/vcfanno

Now at https://github.com/AdamaJava/adamajava

Package OptiTypePipeline

add hisat2_extract_splice_sites.py to the hisat2 package

Pacakge MutliQC
https://github.com/ewels/MultiQC

package sailfish
https://github.com/kingsfordgroup/sailfish

package stringtie - done: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=924101

package kallisto

package r-wasabi
https://github.com/COMBINE-lab/wasabi

package oncofuse
https://github.com/mikessh/oncofuse

package hts_nim_tools
https://github.com/brentp/hts-nim-tools

package Python module geneimpacts

package seqcluster
https://github.com/lpantano/seqcluster/archive/1824d37.tar.gz

package pizzly
https://github.com/pmelsted/pizzly
including pizzly_flatten_json.py

package vt
https://github.com/atks/vt

package fgbio
https://github.com/fulcrumgenomics/fgbio
