Commit ad9a0638 authored by Jacques Lagnel's avatar Jacques Lagnel
Browse files

update README

parent 42bdcd08
......@@ -10,6 +10,13 @@
c) merge the 2 bam file
### 5) mapping QC report (multiqc)
### 6) SNPs calling using GATK in parallel mode: reference splitted by sequences: #tasks=#samples X #chrs
#### a) GATK using "Best Practices Workflows" https://gatk.broadinstitute.org/hc/en-us/sections/360007226651-Best-Practices-Workflows
#### b) using hard filtering as outlined in GATK docs
#### https://gatkforums.broadinstitute.org/gatk/discussion/2806/howto-apply-hard-filters-to-a-call-set
#### https://gatk.broadinstitute.org/hc/en-us/articles/360035890471-Hard-filtering-germline-short-variants
## Snakemake features: fastq from csv file, config, modules, SLURM
### Workflow steps are descibed in the dag_rules.pdf
......
......@@ -106,6 +106,7 @@ rule fastp_pe:
html = config["outdir"]+"/fastp/{sample}_trim.html"
shell:
"""
if
date
cat {input.R1} >{params.spl}.r1.fq.tmp.gz
date
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment