bcftools mpileup -f ../bwa/chr8.fna ../bwa_mem/marked.bam |  bcftools call -mv -o file.vcf 

bcftools stats file.vcf > file_stats.txt

bcftools filter -i'%QUAL>30 && DP>50' file.vcf -o filtered_file.vcf

bcftools stats filtered_file.vcf > filtered_stats.txt

bedtools genomecov -bg -ibam ../bwa_mem/marked.bam > genomecov_chr8.bed

awk '{if($4 > 50) {print $1"\t"$2"\t"$3"\t"$4}}' genomecov_chr8.bed > 50_chr8.bed

wc -l 50_chr8.txt

cp file_stats.txt ~/public_html/term3/block3/pr13

cp filtered_stats.txt ~/public_html/term3/block3/pr13