From e7a57b00c3033c0cdc7c9ab769128e518483da34 Mon Sep 17 00:00:00 2001 From: Yutian Feng Date: Thu, 18 Oct 2018 17:47:57 -0400 Subject: [PATCH] Delete varsnps.sh --- varsnps.sh | 27 --------------------------- 1 file changed, 27 deletions(-) delete mode 100644 varsnps.sh diff --git a/varsnps.sh b/varsnps.sh deleted file mode 100644 index 4bdbfad..0000000 --- a/varsnps.sh +++ /dev/null @@ -1,27 +0,0 @@ -#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