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If an alignment file is a single BAM file across the genome, --in [inputReads].bam can be used to take the BAM file as input.
If an alignment file is a single BAM file across the genome, --in [inputReads].bam can be used to take the BAM file as input.
==== Multiple files separated by chromosomes ===
==== Multiple files separated by chromosomes ====
If the alignment file is split per chromosome (as in 1000 genomes project BAM file), --inprefix [prefix] --insuffix [suffix] should be used to take the BAM input files.
If the alignment file is split per chromosome (as in 1000 genomes project BAM file), --inprefix [prefix] --insuffix [suffix] should be used to take the BAM input files.
