update README

README.md

@@ -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

Snakefile_para_gatk_PEmerged.smk

@@ -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