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Bash #2

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AnnaPNM Jan 26, 2023
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AnnaPNM Jan 26, 2023
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2 changes: 0 additions & 2 deletions README.md
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27 changes: 27 additions & 0 deletions bash_script_Anna.sh
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#!/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
34 changes: 34 additions & 0 deletions vcf results.vcf
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##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