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Mapping pipeline

First log into the serve
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 [email protected] 10 -b - | samtools sort [email protected] 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'