Latest version on Fourierseq: 0.1.18 installed 9/26/11 by SPHS
Useful samtools utilies:
1. samtools idxstats : This tool will provide statistics about how many reads have aligned to each sequence/chromosome in the reference genome. The input bam file must be sorted and indexed.
2. samtools flagstat : Simple stats about how many reads mapped to the reference, how many reads were paired properly etc. The input bam file must be sorted and indexed.
1. samtools mpileup -Euf 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. Note that as of late 2011, the new BAQ filter seems to aggressively remove SNPs unless you "extend" it with the "-E" option.
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