graph TB
analysisDir ---->fq
analysisDir-->sample.list.txt
fq-->*.R1.fq.gz
fq-->*.R2.fq.gz
analysisDir ---->genome
genome-->sequences.fa
genome-->genes.gtf
install dependencies using conda:
mamba create -n WGS perl=5.26.2 gatk4=4.2.5 bwa=0.7.17 samtools=1.15 vcftools=0.1.16 snpeff=5.1 python=3.7 parallel=20211222 bcftools=1.15 multiqc=1.12
#activate environment
conda activate WGS
#change working directory to analysisDir
cd /mnt/d/workshop/3.ReSeq
#run
bash onekeyReseq
directory | meaning |
---|---|
1.mapping | mapping resultsmapStat.html is the analysis report |
2.SNP | SNP/InDel Resultssnp.indel.anno.addid.vcf is the final variant file |
commands | .sh is the detail commands .sh.ok means the step is done normally |
log | log filesstdout.log is the log of standard output,stderr.log is the log of standard error |