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workspace:cloud_sdk_docker | cnmops_docker | condense_counts_docker | gatk_docker | gatk_docker_pesr_override | genomes_in_the_cloud_docker | linux_docker | manta_docker | samtools_cloud_docker | sv_base_docker | sv_base_mini_docker | sv_pipeline_base_docker | sv_pipeline_docker | sv_pipeline_hail_docker | sv_pipeline_updates_docker | sv_pipeline_qc_docker | sv_pipeline_rdtest_docker | wham_docker | ref_panel_name | ref_panel_bincov_matrix | ref_panel_contig_ploidy_model_tar | ref_panel_cutoffs | ref_panel_del_bed | ref_panel_dup_bed | ref_panel_gcnv_model_tars_list | ref_panel_genotype_pesr_pesr_sepcutoff | ref_panel_genotype_pesr_depth_sepcutoff | ref_panel_genotype_depth_pesr_sepcutoff | ref_panel_genotype_depth_depth_sepcutoff | ref_panel_ped_file | ref_panel_PE_files_list | ref_panel_PE_metrics | ref_panel_qc_definitions | ref_panel_requester_pays_crams | ref_panel_samples_list | ref_panel_SD_files_list | ref_panel_SR_files_list | ref_panel_SR_metrics | ref_panel_std_manta_vcf_tar | ref_panel_std_wham_vcf_tar | ref_panel_vcf | reference_name | reference_allosome_file | reference_autosome_ |
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phaseSets <- read.table("phase_sets.dat", header=T) | |
switches <- read.table("compare.err_pos.more") // this file is created by the phasing evaluation scripts | |
names(switches) <- c("POS", "TYPE") | |
phaseSets$MID <- (phaseSets$START + phaseSets$END) / 2 | |
phaseSets$COLOR <- factor(seq(1,dim(phaseSets)[1]) %% 4) | |
phaseSets$LABEL <- ifelse(phaseSets$NUM_SITES > 500, phaseSets$NUM_SITES, NA) | |
ggplot(phaseSets) + | |
geom_segment(aes(y=1, yend=1, x=START, xend=END, color=COLOR), size=4) + |
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#!/bin/env python | |
import fileinput | |
idx = 1 | |
samples = [] | |
for line in fileinput.input(): | |
if line.startswith("##"): | |
continue | |
if line.startswith("#CHROM"): |
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library(GenomicRanges) | |
library(rtracklayer) | |
library(bsseq) | |
library(Homo.sapiens) | |
# methylation summaries are data frames with columns, "chr", "start", "strand", "meth", "unmeth" | |
# get them all in one data frame | |
mergedSummary <- merge(normalMethylationSummary, cancerMethylationSummary, | |
by=c("chr", "start", "strand", "end"), |