BED files usage a beginners query!

Question

[mital.bhatt14]

How to use .bed files for variant calling, at which stage? Which are the suitable tools and commands?

Answer 1

[Pierre Lindenbaum]

BED files are used to call the variant sin a set of defined regions.

which are the suitable tools and commands?

read the numerous manuals for NGS variant calling.

[mital.bhatt14]

Thank you!

Answer 2

[JustinZhang]

Probes are made for some genome region you are interested in. The region outside your interest is usually filtered because the data quality of it is not guaranteed, or it does have nothing to do with your study/diagnosis design.

It's to say, you need a bed file to limit your analysis range.

---

Take somatic targeted oncopanel seqencing as example,

designed panel size > panel size where somatic variants reported >= panel size to calculate biomarkers (TMB, MSI, etc)

---

In that the whole human genome reference sequence is need for mapping to avoid bias, technically you can use bed file any time after mapping.

[mital.bhatt14]

Thank you ! I have a .bed file from manufacturer, but when i use it for checking coverage with my .bam file, it gives error. I have figured out now the root of this was in reference genome. I have doubt however now in BAIT intervals and Target Intervals. How can I design that and use it? Thank you in anticipation

[JustinZhang]

If your "design" term means to customize an unique panel covering genomic regions you are interested in, I suggest you turn to manufacturers for help, such as Agilent. Routinely, you show them your gene list, and they do the left for you, and you will not know the detail.

---

How to design your gene list? It's based on your research goal. No one expect yourself can figure out it.

---

How to convert a gene list to probes covering specific genomic region? It's somewhat business secret. If you wanna know the basic principle, read a PCR tutorial or molecular biology laboratory techniques lesson.