Page tree
Skip to end of metadata
Go to start of metadata

You are viewing an old version of this page. View the current version.

Compare with Current View Page History

« Previous Version 20 Next »

Samtools

Setup output directory.

mkdir samtools

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/ 
cp bowtie/REL606.5.fasta samtools/

Index the reference file.

samtools faidx samtools/REL606.5.fasta

Convert from SAM to BAM format.

samtools view -bS -o samtools/REL606.5.bam bowtie/REL606.5.sam |borderStyle=solid}

Sort the BAM file.

samtools sort samtools/REL606.5.bam samtools/sorted_REL606.5

Output VCF file.

samtools mpileup -uf samtools/REL606.5.fasta samtools/sorted_REL606.5.bam \|bcftools view -vcg - \> samtools/output.vcf 

Produces output.vcf from Bowtie and output.vcf from BWA.

Move all 3(question) bam files and all 3(question) vcf files to lonestar
introduce bedtools.

  • No labels