View met_cnvs.txt
| 2-584759 no MET | |
| 2-584751 MET (FISH and ddPCR) | |
| 2-584699 MET (FISH and ddPCR) |
chapmanb
/ bcbio_vm_install.sh
Created Jan 29, 2019
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 |
chapmanb
/ Seracare_CNV_control_a-normalized.cnr
Created Dec 12, 2018
CNVkit Seracare CNV segmentation
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 |
chapmanb
/ bcbio-cromwell-gcp.conf
Created Dec 9, 2018
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 |
chapmanb
/ sacCer3.chrom.sizes
Created Nov 20, 2018
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
/ 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
/ 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 { |
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
/ 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 . |
NewerOlder