Coverage analysis

Initialize SeQuiLaSession and download sample data (check Initialize section for details)

%run initialize.ipynb

coverage

coverage(tableName: String, sampleId: String, refPath: String)

Compute reads coverage over using aligment data

input parameters

• tableName - registered table over alignment files (see File formats for details)

• sampleId - name of the sample correspondind to the name of the alignment file without a file extension

• refPath - path to the reference file

returned columns

Blocks or based-level of coverage with the following columns:

• sample_id - name of the sample correspondind to the name of the alignment file without a file extension

• contig - contig name

• pos_start - start postition of a block

• pos_end - end postition of a block

• coverage - depth of coverage for a block or single position

ss.sql(f"SELECT * FROM coverage('{table_name}','{sample_id}', '{ref_path}') LIMIT 5").toPandas()

	contig	pos_start	pos_end	ref	coverage
0	1	34	34	R	1
1	1	35	35	R	2
2	1	36	37	R	3
3	1	38	40	R	4
4	1	41	49	R	5

In order to include positions(organized in blocks or base-level) with depth of coverage equal 0 you can set the following parameter:

ss.sql("SET spark.biodatageeks.coverage.allPositions=true")
ss.sql(f"SELECT * FROM coverage('{table_name}','{sample_id}', '{ref_path}') LIMIT 5").toPandas()

	contig	pos_start	pos_end	ref	coverage
0	1	34	34	R	1
1	1	35	35	R	2
2	1	36	37	R	3
3	1	38	40	R	4
4	1	41	49	R	5

For more details on other coverage related parameters including reads filtering please refer to SeQuiLa documentation

ss.stop()