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

Both are available at

Code Block
/corral-repl/utexas/BioITeam/ngs_course/local/data/mapping_example/scripts

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 

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Code Block
titleMapping with BWA - bwa_samtools.sh
#!/usr/bin/env bash

#BWA
mkdir bwa 
bp_seqconvert --from genbank --to fasta <REL606.5.gbk > bwa/REL606.5.fasta
bwa index bwa/REL606.5.fasta
bwa aln -f bwa/SRR030257_1.sai bwa/REL606.5.fasta SRR030257_1.fastq
bwa aln -f bwa/SRR030257_2.sai bwa/REL606.5.fasta SRR030257_2.fastq
bwa sampe -f bwa/REL606.5.sam bwa/REL606.5.fasta bwa/SRR030257_1.sai bwa/SRR030257_2.sai SRR030257_1.fastq SRR030257_2.fastq

#Samtools
mkdir bwa_samtools
cp bwa/REL606.5.sam bwa_samtools/ 
cp bwa/REL606.5.fasta bwa_samtools/
samtools faidx bwa_samtools/REL606.5.fasta
samtools view -bS -o bwa_samtools/REL606.5.bam bwa/REL606.5.sam 
samtools sort bwa_samtools/REL606.5.bam bwa_samtools/sorted_REL606.5
samtools mpileup -uf bwa_samtools/REL606.5.fasta bwa_samtools/sorted_REL606.5.bam \|bcftools view -vcg - \> bwa_samtools/output.vcf 

Both are available at

Code Block
/corral-repl/utexas/BioITeam/ngs_course/local/data/mapping_example/scripts