samtools mpileup -uf samtools_bowtie/REL606.5.fasta samtools_bowtie/sorted_REL606.5.bam \|bcftools view -vcg - \> samtools_bowtie/output.vcf
VCF format has Allele Frequency tags denoted by AF1. Try the following command to see what values we have in our files.
What does the -v flag do in grep?
cat input.vcf | grep AF1=1 > output.vcf
Is not practical, since we will lose vital VCF formatting and may not be able to use this file in the futre.
cat input.vcf | grep -v AF1=0 > output.vcf
Will preserve all lines that don't have an AF1=0 value and is one way of doing this.
sed -i '/AF1=0/ d' input.vcf
Determining Differences Between Aligners.