Visualizing exome Sequencing data for depth

Question

[ruhirai]

Hi I have about 80 samples. I ran GATK on it to do DepthofCoverage on it and generated all the following files

Coverage_summary
Coverage_summary.sample_cumulative_coverage_counts
Coverage_summary.sample_cumulative_coverage_proportions
Coverage_summary.sample_interval_statistics
Coverage_summary.sample_interval_summary
Coverage_summary.sample_statistics
Coverage_summary.sample_summary

I want to create a table with all samples showing Sample ID, targeted regions, depth for forward read, Depth for reverse read, Median Depth for that target

And then I want to be able to plot this data showing per sample median depth per targeted region.

Any suggestion is appreciated

Thank you

Answer 1

[Gungor Budak]

Hi!

You can do this with samtools depth easily.

samtools depth can work with multiple inputs and it generates such a file with the below command:

Command (please see official docs for arguments, you will probably need to provide forward and reverse reads from BAMs separately)

samtools depth -r 1 -m 100 -Q 20 -q 10 -a bam1 bam2 bam3

Output

1   55475000    38  49  58
1   55475001    37  50  57
1   55475002    36  51  55
1   55475003    38  52  55
1   55475004    36  51  56
1   55475005    35  51  55
1   55475006    35  51  54
1   55475007    35  51  55
1   55475008    35  54  51
1   55475009    35  53  56
1   55475010    34  53  53
1   55475011    35  53  56
1   55475012    36  53  55
1   55475013    35  54  56
1   55475014    36  55  59
1   55475015    35  55  58
1   55475016    34  49  54
1   55475017    34  53  55
1   55475018    35  54  54
1   55475019    34  50  54
1   55475020    35  54  56
1   55475021    36  54  59
1   55475022    35  55  60
1   55475023    34  55  59
1   55475024    35  51  58
1   55475025    34  51  59
1   55475026    34  50  60
1   55475027    33  49  57
1   55475028    33  50  58
1   55475029    33  50  58
1   55475030    32  51  57
1   55475031    31  51  59
1   55475032    29  50  59
1   55475033    28  49  55
1   55475034    28  49  55

Finally, use a Python script for example to read every position collect per sample metrics and calculate mean, median, etc. Following is a sample code for my previous analysis (for a similar purpose, not exactly the same).

import sys
import numpy as np

print('\t'.join([
    '#chrom', 'pos', 'mean', 'median',
    '1', '5', '10', '15', '20', '25',
    '30', '50', '100']))
with open(sys.argv[1]) as rows:
    for row in rows:
        row = row.strip().split()
        print('\t'.join(row[0:2]), end='\t')
        covs = np.array(list(map(int, row[2:])))
        two_decimals = '%.2f'
        four_decimals = '%.4f'
        above_1 = np.size(np.where(covs >= 1)) / np.size(covs)
        above_5 = np.size(np.where(covs >= 5)) / np.size(covs)
        above_10 = np.size(np.where(covs >= 10)) / np.size(covs)
        above_15 = np.size(np.where(covs >= 15)) / np.size(covs)
        above_20 = np.size(np.where(covs >= 20)) / np.size(covs)
        above_25 = np.size(np.where(covs >= 25)) / np.size(covs)
        above_30 = np.size(np.where(covs >= 30)) / np.size(covs)
        above_50 = np.size(np.where(covs >= 50)) / np.size(covs)
        above_100 = np.size(np.where(covs >= 100)) / np.size(covs)
        data = [
            two_decimals % np.mean(covs),
            two_decimals % np.median(covs),
            four_decimals % above_1,
            four_decimals % above_5,
            four_decimals % above_10,
            four_decimals % above_15,
            four_decimals % above_20,
            four_decimals % above_25,
            four_decimals % above_30,
            four_decimals % above_50,
            four_decimals % above_100
        ]
        print('\t'.join(data), end='\n')