Changes

{{{hdr|===}}} Bam Index File (<code>--bamIndex</code>) {{{hdr|===}}}

{{{hdr|===}}} Bam Index File ({{#if: {{{noParam|}}} | {{{noParam}}} argument|<code>{{{param|--bamIndex}}}</code>}}) {{{hdr|===}}}

Use <code>--bamIndex</code> followed by your file name to specify the BAM index file to use for reading the BAM file.

{{#if: {{{noParam|}}} | The {{{noParam}}} argument is the name of the BAM index file to use for reading the BAM file.|Use <code>{{{param|--bamIndex}}}</code> followed by your file name to specify the BAM index file to use for reading the BAM file.}}

If this file is required but not specified, it will use the input file name + ".bai".

{{#if: {{{required|}}} | |If this file is required but not specified, it will use the input file name + ".bai".}}