How To Set A Threshold On Mapping Quality

Question

[Junfeng]

Hi, we know that the reliable alignments can be obtained by setting a threshold on mapping quality, such as: samtools view -bq 1 aln.bam > aln.reliable.bam. Here i want to know how to set the threshold? Is there any standard method for this setting? Thank you.

[Junfeng]

Thanks for editing my question so that it's easy to read.

[caro-ca]

Hi!! I'm trying to detect deletions of transposons by looking at the bam files of the alignments between the reference genome and the fastq pairs, and the annotation of the TEs. The mapper I used is STAR and for the visualization I used IGV. In this context, I need to set a quality value threshold in order to remove noise. So far I haven't found the minimum mapping quality score. Any help would be appreciated. Thank you in advance for your time.

[ATpoint]

Please do not ask unrelated questions in old threads. Open a new question. In your case, by-eye analysis is probably not meaningful I guess. Use a proper variant caller. I often see MAPQ set to 20, check the literature and manuals of the variant callers.

Answer 1

[Junfeng]

It seems that we do not need to care about this (set it as 1 is enough) if we just want to detect SNPs (http://maq.sourceforge.net/qual.shtml). Is this correct?