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Old 10-26-2017, 02:20 AM   #1
biomolgen
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Location: Germany

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Default Is there a limit for SAMTOOLS tview option?

Hi all,

I am new to the genomics field and I have recently started working with SAMTOOLS. My question is the following:

I have my SAM file with 2,5 M aligned reads.
I convert it to BAM file with SAMTOOLS
I make the index of the BAM and the reference file

What I want to do is use the tview command to study a region of interest (say position 150-160). So I write this:

Code:
samtools tview -d T -p ref_cons:145 BAM_FILE --reference REFERENCE_FILE
It works fine, BUT the problem is that it returns only ~8,000 lines (reads). My question then is if there is some limit of the number of alignments that are outputted and, if so, how can I make it so that it prints all of them?

Thank you!
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Old 10-26-2017, 03:18 AM   #2
GenoMax
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Default

Cross-posted and answered on Biostars: https://www.biostars.org/p/279942/
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