navigate IGV to the points of interest

Question

[marongiu.luigi]

Dear all,

would be possible to point directly IGV to the positions that contain reads? That is, how to navigate to the point(s) of interest?

I have an alignment with few (if any) reads mapped to a given genome that is several million bp in length. From IGV's manual, I see that one could

a. manually move the chromosome ideogram with the mouse

b. use the left and right arrows

c. use the home and end keys

But with few reads and a wide genome, this means manually checking the whole length of the genome to find some sparse alignments. Since the minimal length to visualize the reads has been set to 30 kB, this process can be tedious and error-prone.

Is there a way to move IGV to the positions that contain reads?

Or is there another way to extract the position of the mapped reads, maybe through a samtool table?

The characteristics of the alignment I have are:

$ samtools flagstat <file>.bam
10542623 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
66331 + 0 supplementary
0 + 0 duplicates
10125616 + 0 mapped (96.04% : N/A)
10476292 + 0 paired in sequencing
5238146 + 0 read1
5238146 + 0 read2
9569512 + 0 properly paired (91.34% : N/A)
10057678 + 0 with itself and mate mapped
1607 + 0 singletons (0.02% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

Thank you

Answer 1

[Tm]

You can first convert your BAM file in to BED file using bamtobed and can get position of chromosomes where reads are mapped.

[Madelaine Gogol]

Yeah, and then you could also use a batch file to automate jumping to those regions, maybe: https://software.broadinstitute.org/software/igv/batch