Setup output directory.
If you do not have an alignment file in the SAM format you may want to start with Introduction to mapping.
cp bowtie/REL606.5.sam samtools_bowtie/ cp bowtie/REL606.5.fasta samtools_bowtie/
Index the reference file.
samtools faidx samtools_bowtie/REL606.5.fasta
Convert from SAM to BAM format.
samtools view -bS -o samtools_bowtie/REL606.5.bam bowtie/REL606.5.sam |borderStyle=solid}
Sort the BAM file.
samtools sort samtools_bowtie/REL606.5.bam samtools_bowtie/sorted_REL606.5
Output VCF file.
samtools mpileup -uf samtools_bowtie/REL606.5.fasta samtools_bowtie/sorted_REL606.5.bam \|bcftools view -vcg - \> samtools_bowtie/output.vcf
Produces output.vcf from Bowtie and output.vcf from BWA.
Move all 3 bam files and all 3 vcf files to lonestar
VCF format has Allele Frequency tags denoted by AF1. Try the following command to see what value we have in our files.
cat input.vcf | grep AF1
For the data we are dealing with, predictions with an allele frequency not equal to 1 are not really applicable. How can we remove these lines from the file and continue on?
What does the -v flag do in grep?
Is not practical, since we will lose vital VCF formatting and may not be able to use this file in the futre.
Will preserve all lines that don't have an AF1=0 value and is one way of doing this.
Is a better way of doing it inline and not requiring you to make another file.
Bedtools is a suite of utility programs that work on a variety of file formats, one of which is conveniently VCF format. Using intersectBed and subtractBed we can find equal and different predictions between mappers.
module load bedtools
Finding alike mutations.
intersectBed -a bowtie.vcf -b bwa.vcf > intersect.vcf
Finding unique mutations for each mapper.
subtractBed -a bowtie.vcf -b intersect.vcf > unique_bowtie.vcf subtractBed -a bwa.vcf -b intersect.vcf > unique_bowtie.vcf