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.IX Title "CONVERT-SAM-FOR-RSEM 1"
.TH CONVERT-SAM-FOR-RSEM 1 2024-03-24 "perl v5.38.2" "User Contributed Perl Documentation"
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.SH NAME
convert\-sam\-for\-rsem \- Make a RSEM compatible BAM file.
.SH SYNOPSIS
.IX Header "SYNOPSIS"
.Vb 1
\& convert\-sam\-for\-rsem [options] <input.sam/input.bam/input.cram> output_file_name
.Ve
.SH ARGUMENTS
.IX Header "ARGUMENTS"
.IP \fBinput.sam/input.bam/input.cram\fR 4
.IX Item "input.sam/input.bam/input.cram"
The SAM/BAM/CRAM file generated by user's aligner. We require this file contains the header section.
.IP \fBoutput_file_name\fR 4
.IX Item "output_file_name"
The output name for the converted file. 'convert\-sam\-for\-rsem' will output a BAM with the name 'output_file_name.bam'.
.SH OPTIONS
.IX Header "OPTIONS"
.IP "\fB\-p/\-\-num\-threads\fR <int>" 4
.IX Item "-p/--num-threads <int>"
Set the number of threads to be used for converting. (Default: 1)
.IP "\fB\-\-memory\-per\-thread\fR <string>" 4
.IX Item "--memory-per-thread <string>"
Set the maximum allowable memory per thread. <string> represents the memory and accepts suffices 'K/M/G'. (Default: 1G)
.IP \fB\-h/\-\-help\fR 4
.IX Item "-h/--help"
Show help information.
.SH DESCRIPTION
.IX Header "DESCRIPTION"
This program converts the SAM/BAM/CRAM file generated by user's aligner into a BAM file which RSEM can process. However, users should make sure their aligners use 'reference_name.idx.fa' generated by 'rsem\-prepare\-reference' as their references and output header sections. After the conversion, this program will call 'rsem\-sam\-validator' to validate the resulting BAM file.
.PP
Note: You do not need to run this script if `rsem\-sam\-validator' reports that your SAM/BAM/CRAM file is valid.
.SH EXAMPLES
.IX Header "EXAMPLES"
Suppose input is set to 'input.sam' and output file name is "output"
.PP
.Vb 1
\& convert\-sam\-for\-rsem input.sam output
.Ve
.PP
We will get a file called 'output.bam' as output.