How to calulate base counts percentage?

KuoshengKuosheng TaiwainMember
edited July 2015 in Ask the GATK team

Hi, I using DepthOfCoverage to count base counts of my bam file and I got the information as list:

Locus Total_Depth Average_Depth_sample Depth_for_sample mane sample mane_base_counts
1:27059142-27059298:1 482 482.00 482 A:1 C:481 G:0 T:0 N:0
1:27059142-27059298:2 482 482.00 482 A:482 C:0 G:0 T:0 N:0
...

And I want to transfer count number to percentage such as:
1:27059142-27059298:1 482 482.00 482 A:0.2 C:99.8 G:0 T:0 N:0
1:27059142-27059298:2 482 482.00 482 A:100 C:0 G:0 T:0 N:0
..

Here "A:0.2" is 1/482100, "C:99.8" is 481/482100, and "A:100" is 482/482*100.

So how can I do that after DepthOfCoverage??

Thanks

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Comments

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @Kuosheng
    Hi,

    I don't think there is a GATK tool to do that. You may have to write your own script to convert to percentages if there is no other tool to do it for you.

    -Sheila

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