Page tree

Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

Setup output directory.

Code Block
mkdir bowtie_samtools

If you do not have an alignment file in the SAM format you may want to start with Introduction to mapping.

Code Block
cp bowtie/REL606.5.sam bowtie_samtools/ 
cp bowtie/REL606.5.fasta bowtie_samtools/

Index the reference file.

Code Block
samtools faidx bowtie_samtools/REL606.5.fasta

Convert from SAM to BAM format.

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

Sort the BAM file.

Code Block
samtools sort bowtie_samtools/REL606.5.bam bowtie_samtools/sorted_REL606.5

Output VCF file.

Code Block
samtools mpileup -uf bowtie_samtools/REL606.5.fasta bowtie_samtools/sorted_REL606.5.bam \|bcftools view -vcg - \> bowtie_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.

...