Detecting Structural Variant From Chip Seq Data

Question

[sara]

Hi,

I am newbie to NGS data analysis.

I used BWA for aligning to reference genome and then samtool. Now am having bam file, sam file and VCF file. i used IGV browser to view the bam file in than i seen IGV uses color coding to flag anomalous insert sizes.

Red for an inferred insert size that is larger than expected (deletion) Blue for an inferred insert size that is smaller than expected (insertion)

i need to extract the deletion part from the bam file or samfile. can anybody give a suggestion of tools on how to extract this particular region ?

Answer 1

[Sean Davis]

Some choices to try might include breakdancer (pe), delly (pe and sr), pindel (sr), and cnvnator (rd) where pe = paired-end, sr = split read, and rd = read depth. There are MANY other options and I would be reluctant to suggest which would be "best" for any given situation.

[PoGibas]

Won't it be a problem to detect SV using chip-seq data? I though that chip-seq covers too short regions for SV calling.

[Sean Davis]

I agree that the false-negative rate may be very high, but for all but the read-depth approaches, there is at least the potential for these softwares to find something if it is present in the data. The original poster seems to believe that she can see a signal by eye.

[sara]

@ Sean Davis, through visualization only i seen the signal. Since am new to this field i need help from expertise.