Mapping pipeline

First log into the serve

ssh monica@10.18.0.21

Then go to the correct directory with the data:

cd /opt/storage5/monica/NGS_data

If you have a new reference you have to index it using:

bwa index <reference_file>

Perform mapping using the following code

bwa mem -t 10 -R "@RG\tID:AGT12\tSM:ATG12\tPL:Illumina" Anopheles_gambiae.AgamP4.dna.toplevel.fa AGT12_1.fastq.gz AGT12_2.fastq.gz | samtools view -@ 10 -b - | samtools sort -@ 10 -o AGT12.bam -

Then index the bam file with

samtools index AGT12.bam

Create a table of variants

 bcftools mpileup -f Anopheles_gambiae.AgamP4.dna.toplevel.fa AGT12.bam | bcftools call -mv | bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%TGT]\n'