Summarize the subject metadata available for bam files¶

I'm a developer, and I have written a new mutation calling pipeline. I've tested it on my own small dataset, but now I'm looking for a larger set of bam files that I can run through it.

First, decide what column to search. I'm looking for columns that are part of the file table:

In [2]:

columns(table="file")

columns(table="file")

Out[2]:

Loading ITables v2.8.1 from the init_notebook_mode cell... (need help?)

file_format is what I'm looking for. Now I want to see whether bam is a valid value in it:

In [3]:

column_values("format")

column_values("format")

Out[3]:

Loading ITables v2.8.1 from the init_notebook_mode cell... (need help?)

The value in the database is BAM, so I'm going to use that. According to the column values, there's around 200 thousand files, but I'm interested in comparing variants for individuals, so I want a count of how many subjects have bam files:

In [4]:

get_subject_data( match_all=["format = bam"])

get_subject_data( match_all=["format = bam"])

Out[4]:

Loading ITables v2.8.1 from the init_notebook_mode cell... (need help?)