| details: | |
| - analysis: variant2 | |
| genome_build: GRCh37 | |
| algorithm: | |
| # Alignment parameters | |
| aligner: bwa | |
| recalibrate: false | |
| realign: false | |
| mark_duplicates: true | |
| remove_lcr: false |
| --- | |
| title: "UMCCR Patient Summary" | |
| author: "Oliver Hofmann" | |
| date: "`r Sys.Date()`" | |
| output: | |
| html_document: | |
| theme: readable | |
| toc: false | |
| toc_float: false | |
| code_folding: hide |
Set up result/sample names:
BCINSTALL="/data/projects/punim0010/local/share/bcbio/"
BCRESULT="/data/cephfs/punim0010/data/Results/Avner/WPT-013/final"
BCFINAL="2017-10-19_WPT-013"
BCPOST="/data/cephfs/punim0010/projects/Hofmann_Explore/testrun"
EXTRAS="/data/projects/punim0010/local/share/extras/"
The conduct is based on Titus Brown's version (with his permission).
All members of the lab, along with visitors, are expected to agree with the following code of conduct. We will enforce this code as needed. We expect cooperation from all members to help ensuring a safe environment for everybody.
| 2016-07-27 23:57:53.400 [IPEngineApp] Using existing profile dir: u'/scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/log/ipython' | |
| 2016-07-27 23:57:53.419 [IPEngineApp] Loading url_file u'/scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/log/ipython/security/ipcontroller-1c9737c4-68fd-49be-b74e-85d8bdda4c49-engine.json' | |
| 2016-07-27 23:57:53.461 [IPEngineApp] Registering with controller at tcp://45.113.233.138:59195 | |
| 2016-07-27 23:57:53.623 [IPEngineApp] Starting to monitor the heartbeat signal from the hub every 5010 ms. | |
| 2016-07-27 23:57:53.634 [IPEngineApp] Using existing profile dir: u'/scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/log/ipython' | |
| 2016-07-27 23:57:53.637 [IPEngineApp] Completed registration with id 1 | |
| 2016-07-28 00:14:25.604 [IPEngineApp] WARNING | No heartbeat in the last 5010 ms (1 time(s) in a row). | |
| cat: write error: Broken pipe | |
| cat: write error: Broken pipe | |
| 2016-07-28 00:20:01.180 [IPEngineApp] Exception in apply request: |
We are in the process of troubleshooting a relatively new Illumina X10 installation with different libraries, including Genome in a Bottle NA12878 samples. Preliminary results look comparable to Illumina's Platinum Genome data as well as data from other X10 facilities:
However, we still have to get a handle on our duplication rates. The Xs (and the 4000s) are known to struggle with higher duplication rates due to 'underloaded' flowcells which causes molecules to migrate to nearby empty nanowells which in turn results in an increased optical duplication rate. But even with that caveat duplication rates should be in the 15-20% range whereas ours tend to be quite a bit higher:
> summary(dup)
V1
Min.
| --- | |
| title: "QC Report" | |
| author: "Automatically generated" | |
| date: "tba" | |
| output: | |
| html_document: | |
| toc: true | |
| theme: united | |
| --- |
| qc = read.table(file.path(path_results, "metrics", "metrics.tsv"), | |
| header=T, sep="\t", check.names=F, | |
| colClasses=list("sample"="character")) | |
| rownames(qc) = qc$sample | |
| qc$Mapped_reads_pct = as.numeric(gsub("%", "", qc$Mapped_reads_pct)) | |
| qc$Duplicates_pct = as.numeric(gsub("%", "", qc$Duplicates_pct)) | |
| metrics = c("sample", "Total_reads" ,"Mapped_reads_pct", "Duplicates_pct", | |
| "offtarget", | |
| "%GC", "Sequence_length", "Median_insert_size") |
| library(tidyr) | |
| library(dplyr) | |
| # Import/concat BED coverage files | |
| file_list <- list.files(path='coverage/', pattern='*_coverage_fixed.bed') | |
| for (file in file_list){ | |
| # if the merged dataset does exist, append to it | |
| if (exists("dataset")){ | |
| temp_dataset <-read.table(file.path('coverage', file), |
| Individual filtered VCFs vs filtered standard (variants present in 5/9) samples, `rtg vcfeval -b Shared.vcf.gz -c foo.vcf.gz -t /cm/shared/apps/bcbio/20150720-devel/data/genomes/Hsapiens/GRCh37/rtg/GRCh37.sdf -o eval`: | |
| ``` | |
| File True-pos False-pos False-neg Precision Sensitivity F-measure | |
| filtered.Fresh_4706 3338450 54119 339450 0.9840 0.9077 0.9443 | |
| filtered.Fresh_4707 3409349 154908 268551 0.9565 0.9270 0.9415 | |
| filtered.Fresh_Normal_4708 3464245 190615 213655 0.9478 0.9419 0.9449 | |
| filtered.UMFIX_4085 3134462 145638 543438 0.9556 0.8522 0.9010 | |
| filtered.UMFIX_4090 3101645 105139 576255 0.9672 0.8433 0.9010 | |
| filtered.UMFIX_Normal_4088 3268466 157860 409434 0.9539 0.8887 0.9201 |