NEW VERSION: Commands to use samtools with a bam file, input.bam,
1. samtools mpileup -uf reference.fna aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf
where reference.fna : reference, in fasta format
aln1.bam, aln2.bam : BAM files containing alignment results. You can use 1 or more alignment flies at a time.
2. bcftools view var.raw.bcf | vcfutils.pl varFilter -D10 > var.filtered.vcf
BCFtools does the actual calling of SNPS and the SNP information is stored in var.filtered.vcf. -D option is used to filter by depth of coverage at the SNP location.
Information about VCF file and other filter options at : http://samtools.sourceforge.net/mpileup.shtml
OLD VERSION: Commands to use samtools with a bam file, input.bam,
1. Use samtools pileup to call SNPs
samtools pileup -vcf reference.fna input.bam > out.pileup 2>out.log &
where reference.fna : reference file, in fasta format
input.bam : BAM file containing alignment results
2. Filter the results further by snp quality:
samtools.pl out.pileup||awk '$6>=20' > out.final.pileup