Visualize reads in BAM file

Question

[Prakki Rama]

Dear Biostars,

Could I please know, If there is some way to view the reads in BAM file according to user defined Insert Size range. I would like to visualize all the reads falling between certain Insert Size ranges, not all the reads.

Your ideas and resources would help me a lot. Thanks in advance.

~Prakki Rama.

[ancient_learner]

Check http://bioinf.scri.ac.uk/tablet/help/bam-data-visualization.shtml as well as http://bamview.sourceforge.net/

[Prakki Rama]

Thank you for the link. I tried the tablet, but it does not have an option of visualizing reads that I wanted.

Answer 1

[dariober]

This is a hack but it might be good enough? Parse the input bam to extract alignments within a given *template* size range, here between 0 and 200:

samtools view -h read.pe.bam \
| awk '{if (($0 ~ /^@/) || (sqrt($9^2) > 0 && sqrt($9^2) < 200)) {print $0}}' \
| samtools view -Sb - > insert.bam &&
samtools index insert.bam

Now load insert.bam in your favourite browser.

[Prakki Rama]

Fantastic. This is what I exactly wanted. Thank you very much!

[Prakki Rama]

But every time, we need to run the above script to see what reads mapped for different ranges in different files. Do you have any idea of any tool that by just typing in the insert size range, it will display those reads and automatically remaining reads become greyed or made invisible?

Answer 2

[Ming Tommy Tang]

How about this pybamview

[Prakki Rama]

Hi, thank you for the tool. But, the above script from dariober was catering my need more closely. Thanks.