This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Visualize reads in BAM file

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.

genome bam visualize
• 4,804 views • link
updated by Ram Ram • written by Prakki Rama Prakki Rama

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

• 0 views • link
written by Prakki Rama Prakki Rama

2 answers

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.

• 0 views • link
written by dariober dariober

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

• 0 views • link
written by Prakki Rama 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?

• 0 views • link
written by Prakki Rama Prakki Rama

How about this pybamview

• 0 views • link
updated by Ram Ram • written by Ming Tommy Tang Ming Tommy Tang

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

• 0 views • link
written by Prakki Rama Prakki Rama

Log in to answer this question.

More posts like this