diff --git a/README.md b/README.md
deleted file mode 100644
index 661225e..0000000
--- a/README.md
+++ /dev/null
@@ -1,2 +0,0 @@
-# Final-Project
-Nikita and Oksana are cool
diff --git a/bash_script_Anna.sh b/bash_script_Anna.sh
new file mode 100644
index 0000000..1d9ae1f
--- /dev/null
+++ b/bash_script_Anna.sh
@@ -0,0 +1,27 @@
+#!/bin/sh
+fastqc -outdir ../fastqc/ -t 8 ../../../Data/AI-69_S60_R1_001.fastq.gz ../../../Data/AI-69_S60_R2_001.fastq.gz
+trimmomatic PE -phred33 -threads 8 data/raw_reads/AI-69_S60_R1_001.fastq.gz data/raw_reads/AI-69_S60_R2_001.fastq.gz -baseout trim1 LEADING:15 TRAILING:15 SLIDINGWINDOW:10:20 MINLEN:20
+trimmomatic PE -phred33 -threads 8 data/rawreads/AI-69_S60_R1_001.fastq.gz data/rawreads/AI-69_S60_R2_001.fastq.gz -baseout trim1 LEADING:15 TRAILING:15 SLIDINGWINDOW:10:20 MINLEN:20
+bwa index data/references/T5_sequence.fasta
+fastqc --outdir=../fastqc/ trim1_1P trim1_2P
+bwa mem -t 8 data/references/T5_sequence.fasta data/trims/trim1_1P data/trims/trim1_2P | samtools view -Sb > T5_AI_69_S60_aligned.bam
+mkdir mapped
+mkdir mapped_sorted
+mkdir calling
+mv T5_AI_69_S60_aligned.bam mapped
+samtools sort -@ 8 mapped/T5_AI_69_S60_aligned.bam -o mapped_sorted/T5_AI_69_S60_aligned_sorted.bam
+cd mapped_sorted/
+ls
+cd ../mapped
+samtools view -h T5_AI_69_S60_aligned.bam | head 50
+samtools view -h T5_AI_69_S60_aligned.bam | head -50
+cd ../
+samtools index mapped_sorted/T5_AI_69_S60_aligned_sorted.bam
+bcftools mpileup -Ou -f data/references/T5_sequence.fasta mapped_sorted/T5_AI_69_S60_aligned_sorted.bam | bcftools call -Ou -mv --ploidy 1 | bcftools filter -s LowQual -e '%QUAL<20 || DP>100' > calling/T5_AI_69_S60_variants.vcf
+cd calling/
+rm *
+cd ../
+bcftools mpileup -Ou -f data/reference/T5_sequence.fasta mapped_sorted/T5_AI_69_S60_aligned_sorted.bam | bcftools call -Ou -mv --ploidy 1 | bcftools filter -s LowQual -e '%QUAL<20 || DP>100' > calling/T5_AI_69_S60_variants.vcf
+bcftools mpileup -Ou -f data/references/T5_sequence.fasta mapped_sorted/T5_AI_69_S60_aligned_sorted.bam | bcftools call -Ou -mv --ploidy 1 | bcftools filter -s LowQual -e '%QUAL<20 || DP>100' > calling/T5_AI_69_S60_variants.vcf
+less T5_AI_69_S60_variants.vcf
+exit
\ No newline at end of file
diff --git a/vcf results.vcf b/vcf results.vcf
new file mode 100644
index 0000000..ae78ed4
--- /dev/null
+++ b/vcf results.vcf	
@@ -0,0 +1,34 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##bcftoolsVersion=1.10+htslib-1.10
+##bcftoolsCommand=mpileup -Ou -f data/references/T5_sequence.fasta mapped_sorted/T5_AI_69_S60_aligned_sorted.bam
+##reference=file://data/references/T5_sequence.fasta
+##contig=<ID=T5,length=113951>
+##ALT=<ID=*,Description="Represents allele(s) other than observed.">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of raw reads supporting an indel">
+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of raw reads supporting an indel">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##INFO=<ID=ICB,Number=1,Type=Float,Description="Inbreeding Coefficient Binomial test (bigger is better)">
+##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
+##bcftools_callVersion=1.10+htslib-1.10
+##bcftools_callCommand=call -Ou -mv --ploidy 1; Date=Wed Jan 18 19:05:00 2023
+##FILTER=<ID=LowQual,Description="Set if true: %QUAL<20 || DP>100">
+##bcftools_filterVersion=1.10+htslib-1.10
+##bcftools_filterCommand=filter -s LowQual -e '%QUAL<20 || DP>100'; Date=Wed Jan 18 19:05:19 2023
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	mapped_sorted/T5_AI_69_S60_aligned_sorted.bam
+T5	57822	.	G	A	225	LowQual	DP=243;VDB=0.000940976;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,177,39;MQ=60	GT:PL	1:255,0
+T5	65803	.	GTT	GT	199	LowQual	INDEL;IDV=207;IMF=0.848361;DP=244;VDB=0.959859;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=33,2,167,42;MQ=60	GT:PL	1:226,0