Find Large-scale CNVs in whole exome sequencing

Question

[fifty_fifty]

My ultimate goal is to find malignant cells within all epithelial cells in scRNA-seq data using CONICS algorithm. This method finds large-scale CNVs in each cell based on whole exome sequencing (WES) data. While I work a lot with scRNA-seq data, I have never analyzed WES data. I have matching WES bam files for each sample in scRNA-seq. According to CONICS tutorial, I should use region information from WES with start, end positions and length in each chromosome. They didn't include any WES examples in their tutorials. In absence of WES, they recommend using chromosome position data of the following format:

Idf Chrom   Start   End Length
1   1   0   248956422   122026459
2   2   0   242193529   92188145
3   3   0   198295559   90772458
4   4   0   190214555   49712061
5   5   0   181538259   46485900
6   6   0   170805979   58553888
7   7   0   159345973   58169653
8   8   0   145138636   44033744
9   9   0   138394717   43389635
10  10  0   133797422   39686682
11  11  0   135086622   51078348
12  12  0   133275309   34769407
13  13  0   114364328   16000000
14  14  0   107043718   16000000
15  15  0   101991189   17083673
16  16  0   90338345    36311158
17  17  0   83257441    22813679
18  18  0   80373285    15460899
19  19  0   58617616    24498980
20  20  0   64444167    26436232
21  21  0   46709983    10864560
22  22  0   50818468    12954788

How can I find that kind of data from WES?

[Pierre Lindenbaum]

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[fifty_fifty]

fixed it. thank you!

[GenoMax]

How can I find that kind of data from WES?

You can get chromosome sizes for the genome you are working with from reference. See --> chrom.sizes computed locally

[fifty_fifty]

thank you. How do I find start and end positions?

[GenoMax]

Start can be 0 (or 1 if you are using 1 based indexing) and end would be the length of the chromosome. Check what CONICS needs.

[fifty_fifty]

In their chromosome position file which I copied in my question the end and length do not match. For CONICS I need a list of regions that have evidence for genomic copy number alterations (derived from exome-seq). How do I obtain those regions' positions from WES bam files?