ssh -p 22221 vadim@kodomo.fbb.msu.ru

SRR=SRR10720407
chr=chr21
fastqc=/mnt/scratch/NGS/vadim/fastqc
logdir=/mnt/scratch/NGS/vadim/logdir
paired=/mnt/scratch/NGS/vadim/paired
unpaired=/mnt/scratch/NGS/vadim/unpaired
bamdir=/mnt/scratch/NGS/vadim/bamdir
vcfdir=/mnt/scratch/NGS/vadim/vcfdir
dir_gz=/mnt/scratch/NGS/vadim/${SRR}_1.fastq.gz
rev_gz=/mnt/scratch/NGS/vadim/${SRR}_2.fastq.gz
dir_paired=/mnt/scratch/NGS/vadim/${SRR}_1_paired.fastq.gz
dir_unpaired=/mnt/scratch/NGS/vadim/${SRR}_1_unpaired.fastq.gz
rev_paired=/mnt/scratch/NGS/vadim/${SRR}_2_paired.fastq.gz
rev_unpaired=/mnt/scratch/NGS/vadim/${SRR}_2_unpaired.fastq.gz
indexes=/mnt/scratch/NGS/vadim/reference/${chr}
sam=/mnt/scratch/NGS/vadim/${SRR}.sam
bam=${bamdir}/${SRR}.bam
bam_info=${bamdir}/${SRR}_bam_info.txt
bam_chr=${bamdir}/${SRR}_bam_chr.bam
bam_chr_good=${bamdir}/${SRR}_bam_chr_good.bam
bam_chr_info=${bamdir}/${SRR}_bam_chr_info.txt
vcf=${vcfdir}/${SRR}.vcf
vcf_info=${vcfdir}/${SRR}_vcf_info.txt
vcf_filtered=${vcfdir}/${SRR}_filtered.vcf
vcf_filtered_stats=${vcfdir}/${SRR}_vcf_filtred_stats.txt