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 -uf Euf reference.fna aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf
...
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
...