varLoci

The SCReadCounts release contains a new tool varLoci for enumerating potential variant loci directly from the indexed BAM file. It outputs SNV loci and reference and alternate nucleotides suitable for SCReadCounts SNVs input file.

Usage

% varLoci <bam_file>.bam <min_var_read_count> [ <region> ] > snv_loci.txt

The <bam_file>.bam must be sorted (by alignment start position) and indexed. <bam_file>.bam.bai should be placed in the same directory as the BAM file.

<min_var_read_count> is the minimum number of reads with the variant allele required for a locus to be considered a putative variant loci.

<region> (optional) is the samtools format region specifier. Use <chrom> or <chrom>:<start>-<end> to specify a chromosome or a chromosomal region, respectively. Default: no region constraint.

Notes:

• varLoci is an agressive enumeration of potential variant sites for much more careful analysis by SCReadCounts or other tools. It will, however, provide a much more limited set of loci than an exhaustive enumeration of loci in a genomic region. It will also provide the opportunity for de novo discovery of loci that have not otherwise been annotated elsewhere. Finally, it will avoid the unnecessary examination of annotated loci that are not supported by the data available in the BAM file alignments.
• varLoci requires the BAM file have the MD tag for all alignments in order to determine the reference nucleotide at each locus. Some aligners do not output this tag by default, so look for options that ensure the MD (and NM) tags are output in the BAM file. Alternatively, the following samtools command will add the MD (and NM) tags:

    % samtools calmd -b aln.bam ref.fasta > aln_md.bam
    % samtools index aln_md.bam