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 $BINDIR/bin |
View Seracare_CNV_control_a-normalized.cnr
chromosome start end gene log2 depth weight | |
chr1 500 1094854 Antitarget -0.447257 0.03 0.708181 | |
chr1 1094854 2189208 Antitarget 0.193 0.08 0.869498 | |
chr1 2189708 2189781 FAAP20 0.166003 58.58 0.0757517 | |
chr1 2191894 2192048 FAAP20 0.684696 184.21 0.125722 | |
chr1 2192048 2192202 FAAP20 -0.549982 263.06 0.0954321 | |
chr1 2192202 2192357 FAAP20 0.391232 247.57 0.125377 | |
chr1 2192357 2192511 FAAP20 0.949453 287.09 0.1122 | |
chr1 2192511 2192666 FAAP20 0.496266 206.08 0.113593 | |
chr1 2192666 2192820 FAAP20 0.265958 58.87 0.0857653 |
View bcbio-cromwell-gcp.conf
include required(classpath("application")) | |
system { | |
workflow-restart = true | |
} | |
call-caching { | |
enabled = true | |
} | |
load-control { | |
# Avoid watching memory, since the load-controller stops jobs on local runs |
View sacCer3.chrom.sizes
chrI 230218 | |
chrII 813184 | |
chrIII 316620 | |
chrIV 1531933 | |
chrV 576874 | |
chrVI 270161 | |
chrVII 1090940 | |
chrVIII 562643 | |
chrIX 439888 | |
chrX 745751 |
View tcga_capture.R
#!/usr/bin/env Rscript | |
library(GenomicDataCommons) | |
library(dplyr) | |
manifest = GenomicDataCommons::files() %>% | |
GenomicDataCommons::filter(~ cases.project.project_id == "TCGA-LUAD" & | |
experimental_strategy == "WXS" & | |
data_format == "BAM") %>% | |
GenomicDataCommons::manifest() |
View bcbio-cromwell-http.conf
include required(classpath("application")) | |
system { | |
workflow-restart = true | |
} | |
call-caching { | |
enabled = true | |
} | |
load-control { |
View extract_umis.py
from __future__ import print_function | |
import collections | |
import gzip | |
import sys | |
from Bio.SeqIO.QualityIO import FastqGeneralIterator | |
nbases = 15 | |
nreads = 1e6 | |
toshow = 20 |
View main-arvados_testcwl-pack.cwl
{ | |
"cwlVersion": "v1.0", | |
"$graph": [ | |
{ | |
"class": "Workflow", | |
"hints": [], | |
"inputs": [ | |
{ | |
"id": "#main/config__algorithm__align_split_size", | |
"type": { |
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 . |
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