From Genome Analysis Wiki
Jump to: navigation, search


120 bytes added, 22:17, 8 April 2019
no edit summary
Use <code>{{{param|--in}}}</code> followed by your file name to specify the SAM/BAM input file.}}
The program automatically determines if your input file is SAM/BAM/uncompressed BAM without any input other than a filename from the user{{#if: {{{noStdin|.}}}|, unless your input file is stdin.}}
{{#if: {{{noStdin|This tool does not support input from stdin.}}}|A <code>-</code> is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM).}}
{|border="1" cellspacing="0" cellpadding="2"
| <code>{{#if: {{{noParam|}}} | |--in}} yourFileName</code>
|{{#if: {{{noStdin|}}} | |SAM from stdin}}
| <code>{{#if: {{{noParam|}}} | |--in}} -</code>

Navigation menu