Mapping pipeline

First log into the serve
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ssh [email protected]
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Then go to the correct directory with the data:
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cd /opt/storage5/monica/NGS_data
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If you have a new reference you have to index it using:
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bwa index <reference_file>
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 Perform mapping using the following code
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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 -
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Then index the bam file with
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samtools index AGT12.bam
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Create a table of variants
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 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'
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