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Old 09-07-2011, 09:31 AM   #1
Senior Member
Location: IL

Join Date: Jul 2011
Posts: 100
Default SNP base calling for multiple samples

My goal is to find SNPs from multiple Sanger sequences, which cover varied regions, not necessary the same fragments. When a SNP is found, I want to see the base (or hetero/homo-zygote) of any samples which cover that position. What kind of software should I use? I would prefer a command-line software.

I tried to align sequences via bwasw and pileup all via samtools. However, when I pileuped all samples together, the output did NOT clearly distinguish between when a SNP location not covered in a sample and when a sample had hetero in that SNP location. My commands below.

samtools mpileup -uf Sorbil.fasta a1.bam a2.bam a3.bam | bcftools/bcftools view -bvcg - > raw.bcf

bcftools/bcftools view raw.bcf | varFilter -D100 > flt.vcf
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