Skip to content

Instantly share code, notes, and snippets.

Brad Chapman chapmanb

Block or report user

Report or block chapmanb

Hide content and notifications from this user.

Learn more about blocking users

Contact Support about this user’s behavior.

Learn more about reporting abuse

Report abuse
View GitHub Profile
View met_cnvs.txt
2-584759 no MET
2-584751 MET (FISH and ddPCR)
2-584699 MET (FISH and ddPCR)
View bcbio_vm_install.sh
#!/bin/bash
set -eu -o pipefail
export TARGETDIR=`pwd`/anaconda
export BINDIR=`pwd`
wget http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
bash Miniconda2-latest-Linux-x86_64.sh -b -p $TARGETDIR
$TARGETDIR/bin/conda install --yes -c conda-forge -c bioconda bcbio-nextgen
$TARGETDIR/bin/conda install --yes -c conda-forge -c bioconda bcbio-nextgen-vm
mkdir -p $BINDIR/bin
View Seracare_CNV_control_a-normalized.cnr
chromosome start end gene log2 depth weight
chr1 500 1094854 Antitarget -0.447257 0.03 0.708181
chr1 1094854 2189208 Antitarget 0.193 0.08 0.869498
chr1 2189708 2189781 FAAP20 0.166003 58.58 0.0757517
chr1 2191894 2192048 FAAP20 0.684696 184.21 0.125722
chr1 2192048 2192202 FAAP20 -0.549982 263.06 0.0954321
chr1 2192202 2192357 FAAP20 0.391232 247.57 0.125377
chr1 2192357 2192511 FAAP20 0.949453 287.09 0.1122
chr1 2192511 2192666 FAAP20 0.496266 206.08 0.113593
chr1 2192666 2192820 FAAP20 0.265958 58.87 0.0857653
View bcbio-cromwell-gcp.conf
include required(classpath("application"))
system {
workflow-restart = true
}
call-caching {
enabled = true
}
load-control {
# Avoid watching memory, since the load-controller stops jobs on local runs
View sacCer3.chrom.sizes
chrI 230218
chrII 813184
chrIII 316620
chrIV 1531933
chrV 576874
chrVI 270161
chrVII 1090940
chrVIII 562643
chrIX 439888
chrX 745751
@chapmanb
chapmanb / tcga_capture.R
Created Nov 8, 2018
Query TCGA API for exome capture BED files -- thanks to Sehyun Oh
View tcga_capture.R
#!/usr/bin/env Rscript
library(GenomicDataCommons)
library(dplyr)
manifest = GenomicDataCommons::files() %>%
GenomicDataCommons::filter(~ cases.project.project_id == "TCGA-LUAD" &
experimental_strategy == "WXS" &
data_format == "BAM") %>%
GenomicDataCommons::manifest()
@chapmanb
chapmanb / bcbio-cromwell-http.conf
Created Oct 2, 2018
Cromwell configuration generated by bcbio for http inputs
View bcbio-cromwell-http.conf
include required(classpath("application"))
system {
workflow-restart = true
}
call-caching {
enabled = true
}
load-control {
@chapmanb
chapmanb / extract_umis.py
Created Aug 24, 2018
Extract UMIs from input fastq file
View extract_umis.py
from __future__ import print_function
import collections
import gzip
import sys
from Bio.SeqIO.QualityIO import FastqGeneralIterator
nbases = 15
nreads = 1e6
toshow = 20
View main-arvados_testcwl-pack.cwl
{
"cwlVersion": "v1.0",
"$graph": [
{
"class": "Workflow",
"hints": [],
"inputs": [
{
"id": "#main/config__algorithm__align_split_size",
"type": {
@chapmanb
chapmanb / CCDS_IDTxGEN_SeqCap-hg19.bed
Last active Jun 6, 2018
Combined exome regions files, prepared with hg38 and lifted over to hg19
View CCDS_IDTxGEN_SeqCap-hg19.bed
This file has been truncated, but you can view the full file.
chr1 14395 14616 .
chr1 14672 14802 .
chr1 14832 14992 .
chr1 15012 15148 .
chr1 15611 16024 .
chr1 16541 16877 .
chr1 16893 17032 .
chr1 17251 17374 .
chr1 17403 17519 .
You can’t perform that action at this time.