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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