snpEff: SNP effect predictor a 2nd look

http://snpeff.sourceforge.net/faq.html#I%20sequenced%20a%20genome,%20how%20do%20I%20analyze%20the%20variants?

Am taking a 2nd look at snpeff as a annotation tool for variation. I love programs that post a bash script howto since it mades it dead easy to understand if I can use it for my data or not
e.g. in the example below only the last step is for snpeff, but I have been generating variants using the exact same preceding steps. Anyone else used snpeff before? Want to post comments / reviews?

I sequenced a genome, how do I analyze the variants?

This is an extremelly simplified version on how to analyze the data from scratch (this is not meant to be a tutorial on sequencing analysis).
Let's assume you have sequence data in FASTQ format (file "s.fastq") and your reference genome is dm5.34

 # Download the genome 

wget ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.34_FB2011_02/fasta/dmel-all-chromosome-r5.34.fasta.gz 

gunzip dmel-all-chromosome-r5.34.fasta.gz 

mv dmel-all-chromosome-r5.34.fasta dm5.34.fasta 

# Create a genome index (we assume you installed 

#BWA http://bio-bwa.sourceforge.net/) 

bwa index -bwtsw dm5.34.fasta 

# Map sequences to the genome: Create SAI file 

bwa aln -bwtsw dm5.34.fasta s.fastq > s.sai 

# Map sequences to the genome: Create SAM file 

bwa samse dm5.34.fasta s.sai s.fastq > s.sam 

# Create BAM file (we assume you installed SamTools  

http://samtools.sourceforge.net/) 

samtools view -S -b s.sam > s.bam 

# Sort BAM file (will create s_sort.bam) 

samtools sort s.bam s_sort 

# Create VCF file (BcfTools is part of samtools distribution) 

samtools mpileup -uf dm5.34.fasta s_sort.bam | bcftools view -vcg - > s.vcf 

# Analyze variants using snpEff 

java -Xmx4g -jar snpEff.jar -vcf4 dm5.34 s.vcf > s_snpeff.txt