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Scripts/varsnps.sh
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#requries bcf tools, samtools, and bowtie2 (or other read mapper) | |
bowtie2-build ref.fasta refname | |
#makes bowtie index for reference genome | |
bowtie2 -x refname -1 read1.fq -2 read2.fq -U unpairedread.fq -S output.sam | |
#map reads back to reference genome for sam file | |
samtools view -bS output.sam > output.bam | |
#convert sam to bam | |
samtools sort output.bam -O output.sort.bam | |
#sort by genomic location | |
#need to do next step or the variant annotations are useless | |
samtools mpileup --min-BQ number 20-30 \ | |
-f ref.fasta --BCF bamfromprevious.bam | \ | |
bcftools call --consensus-caller \ | |
--variants-only --pval-threshold 0.05 recommended -Ov -Ob > outputsvariants.bcf ; | |
#gets the variants from read mapping file | |
bcftools norm -m-any outputsvariants.bcf | bcftools norm -Ov --check-ref w -f ref.fasta > outputsvariants.vcf ; | |
#convert to vcf based off of alignment with refernce genome | |
bcftools view outputsvariants.vcf | vcfutils.pl varFilter -d 18 -w 1 -W 3 -a 1 \ | |
-e 0.05 -p > outputsvariants.filtered.vcf ; | |
#filters those variants that don't meet a certain threshold |