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Calculate the median depth of essential genes on chromosome 1
sh run_minimap2.sh # for total reads mapping
# get the depth of each gene from bed files
perl step0_1_samtools_get_bed_depth.argv.pl bam_full.list Leupold_chr1_E_gene.bed bamFull.depth
Downsampling reads
sh count_total_bases.sh
sh seqtk_subreads.sh
Mapping with minimap2
sh run_minimap2.sh
Variant calling with Clair3
sh run_clair3_2_batchly_sample_model_default_options.sh
Merge gvcf files with Glnexus
sh run_glnexus.sh
Variant annotation with SnpEff
# Input file is the merged vcf
sh step01_run_snpeff.sh
perl step02_Step5_extract_snpEff_from_vcf.pl
perl step03_compute_allele_freq.pl
perl step04_combine_snpeff_and_genotype.pl