Maximizing IT Efficiency with Software Asset Management (SAM) Tools
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Maximizing IT Efficiency with Software Asset Management (SAM) Tools

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Market Forecast: Software Asset Management (SAM) tools, 2024-2028, Worldwide
quick SAM to BAM conversion
A postdoc in my lab today was asking me how to compress SAM files back to BAM files. This was apparently nonintuitive to him so I decided to write a quick post on minor details regarding this type of conversion with samtools, a great set of utilities for handling high throughput sequence alignment files:
Before you perform the actual conversion, youâll want to first check if your SAM file contains a header:
head yourFile.sam
If a header exists, you should see lines beginning with â@â. If this is the case, youâll want to use the -b flag to signify the output should be BAM and the -S flag to signify the input is in SAM format. Because the header is present you donât need to include a reference fasta file for samtools to index throughâmeaning you can proceed as follows:
SAM â> BAM if header is present
samtools view  -bS yourFile.sam > youFile.bam
If â@â is missing from the head you did above, youâll want use the -bT flags.Â
SAM â> BAM if header is missing
samtools view -bT reference.fa yourFile.sam > yourFile.bam
Youâll probably want to sort your BAM file, considering sorted BAMs are often the useful files for myriad programs.Â
samtools sort yourFile.bam yourFile_sorted
And lastly, youâll want to index your BAM file as this is also useful for further analyses on your alignments
samtools index yourFile_sorted.bam yourFile_sorted.bai
âŚnow to get back to studying for my qual #distractionsOver #BerekeleyMCBwhyYouDoThis
pipe bowtie samtools
bowtie reference -SC -q .fastq | samtools view -Shu - | samtools sort - name.sorted.prefix samtools index name.sorted.prefix.bam samtools idxstats name.sorted.prefix.bam > stats.txt