holtgrewe

    // ##INFO=<ID=non_cancer_AC_asj_female,Number=A,Type=Integer,Description="Alternate allele count for female samples of Ashkenazi Jewish ancestry in the non_cancer subset">
    // ##INFO=<ID=non_cancer_AN_asj_female,Number=1,Type=Integer,Description="Total number of alleles in female samples of Ashkenazi Jewish ancestry in the non_cancer subset">
    // ##INFO=<ID=non_cancer_AF_asj_female,Number=A,Type=Float,Description="Alternate allele frequency in female samples of Ashkenazi Jewish ancestry in the non_cancer subset">
    // ##INFO=<ID=non_cancer_nhomalt_asj_female,Number=A,Type=Integer,Description="Count of homozygous individuals in female samples of Ashkenazi Jewish ancestry in the non_cancer subset">
    // ##INFO=<ID=AC_raw,Number=A,Type=Integer,Description="Alternate allele count for samples, before removing low-confidence genotypes">
    // ##INFO=<ID=AN_raw,Number=1,Type=Integer,Description="Total number of alleles in samples, before removing low-confidence genotypes">
    // ##INFO=<ID=AF_raw,Num

holtgrewe

    // ##INFO=<ID=AC,Number=A,Type=Integer,Description="Alternate allele count for samples">
    /// Alternate allele count for samples.
    pub ac: Option<i32>,
    // ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in samples">
    /// Total number of alleles in samples.
    pub an: Option<i32>,
    // ##INFO=<ID=AF,Number=A,Type=Float,Description="Alternate allele frequency in samples">
    /// Alternate allele frequency in samples.
    pub af: Option<f32>,
    // ##INFO=<ID=rf_tp_probability,Number=1,Type=Float,Description="Random forest prediction probability for a site being a true variant">

holtgrewe

The setup was done on a recent version of Windows 10 with Windows Subsystem for Linux Version 2 (WSL2).

First, install WSL 2, e.g., following this tutorial

• Note that the whole thing appears to be a bit convoluted, you start out with wsl.exe --install
• Then you can install latest LTS Ubuntu 22.04 with the Microsoft Store
• Once complete, you probably end up with a WSL 1 (one!) that you can conver to version 2 (two!) with wsl --set-version Ubuntu-22.04 2 or similar.
• WSL2 has some advantages including running a full Linux kernel but is even slower in I/O to the NTFS Windows mount.
• Everything that you do will be inside the WSL image.

holtgrewe

diff --git a/etc/kayobe/bifrost.yml b/etc/kayobe/bifrost.yml
index 0bfcec7..00d4651 100644
--- a/etc/kayobe/bifrost.yml
+++ b/etc/kayobe/bifrost.yml
@@ -23,10 +23,10 @@
 # Diskimage-builder configuration.
 
 # DIB base OS element. Default is {{ os_distribution }}.
-#kolla_bifrost_dib_os_element:
+kolla_bifrost_dib_os_element: "centos"

holtgrewe

#!/usr/bin/env python3
"""Tool to cleanup the scratch directories on BIH HPC."""

import argparse
import datetime
import logging
import os
from os.path import join, dirname, normpath, islink, exists, isdir
import pathlib
import re

holtgrewe

#!/usr/bin/env python
# -*- coding: utf-8 -*-

# Note: To use the 'upload' functionality of this file, you must:
#   $ pip install twine

import io
import os
import sys
from shutil import rmtree

holtgrewe

// Term, TermMap, and directly related types ---------------------------------

public interface Prefix extends Serializable {
    public ByteString getValue();
}

public interface TermID extends Comparable <TermID>, Serializable {
    public Prefix getPrefix();
    public int getID();
}

holtgrewe

#!/bin/bash

set -euo pipefail

BAM=
OUT=

print_help()
{
    >&2 echo "USAGE: extract_bam.sh -i IN.bam -o OUT_PREFIX {REGIONS}+"

holtgrewe

; INI file with default data sources for Jannovar.
;
; This file is packed into the Jannovar JAR file.
;
; Each data source is described in one section. By convention, the section
; and data source name is given as "${organism}/${source}". Jannovar will
; serialize the file to "${name}.replace('/', '_').replace("\", "_").
;
; Users can provide their own INI files using the --data-source parameter
; to Jannovar, even orriding the defaults from this file. 

holtgrewe

#!/bin/bash

set -e
set -x

# Source Mercurial repository: http://lemon.cs.elte.hu/hg/lemon
# Target Github repository: https://github.com/seqan/lemon-mirror

# The following is based on the following Stack Overflow help post:
#