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.
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samtools idxstats <in.bam>
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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.
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samtools flagstat <in.bam>
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Example:
1. samtools mpileup -Euf reference.fna aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf
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