SQL
SeQuiLa’s SQL API
Table of Contents
Watchout
Check Configuration page for other configuration options that applicable for all types of APIs.coverage
coverage(table_name , sample_name, ref_path)
Parameters
| Parameter Name | Type | Meaning |
|---|---|---|
| table_name | str | name of the external table created over alignment file(s) in BAM/CRAM format (with an index file - both BAI and SBI are supported) |
| sample_name | str | name of the sample in table_name to use for coverage calculations |
| ref_path | str | the reference file in FASTA format (with an index file) |
Examples
CREATE TABLE IF NOT EXISTS reads
USING org.biodatageeks.sequila.datasources.BAM.BAMDataSource
OPTIONS(path "{{ PWD }}/data/NA12878.bam");
-- calculate coverage
SELECT * FROM coverage('reads', 'NA12878','{{ PWD }}/data/hg18.fasta') LIMIT 10;
+------+---------+-------+---+--------+
|contig|pos_start|pos_end|ref|coverage|
+------+---------+-------+---+--------+
| 1| 34| 34| R| 1|
| 1| 35| 35| R| 2|
| 1| 36| 37| R| 3|
| 1| 38| 40| R| 4|
| 1| 41| 49| R| 5|
| 1| 50| 67| R| 6|
| 1| 68| 109| R| 7|
| 1| 110| 110| R| 6|
| 1| 111| 111| R| 5|
| 1| 112| 113| R| 4|
+------+---------+-------+---+--------+
only showing top 10 rows
coverage
pileup(table_name , sample_name, ref_path, include_quals)
Parameters
| Parameter Name | Type | Meaning |
|---|---|---|
| table_name | str | name of the external table created over alignment file(s) in BAM/CRAM format (with an index file - both BAI and SBI are supported) |
| sample_name | str | name of the sample in table_name to use for coverage calculations |
| ref_path | str | the reference file in FASTA format (with an index file) |
| include_quals | bool(false) | whether to include base qualities pileup as well for positions with alts |
Examples
CREATE TABLE IF NOT EXISTS reads
USING org.biodatageeks.sequila.datasources.BAM.BAMDataSource
OPTIONS(path "{{ PWD }}/data/NA12878.bam");
-- calculate pileup
SELECT * FROM pileup('reads', 'NA12878','{{ PWD }}/data/hg18.fasta', false) LIMIT 5;
+------+---------+-------+---------+--------+--------+-----------+----+-----+
|contig|pos_start|pos_end| ref|coverage|countRef|countNonRef|alts|quals|
+------+---------+-------+---------+--------+--------+-----------+----+-----+
| 1| 34| 34| C| 1| 1| 0|null| null|
| 1| 35| 35| C| 2| 2| 0|null| null|
| 1| 36| 37| CT| 3| 3| 0|null| null|
| 1| 38| 40| AAC| 4| 4| 0|null| null|
| 1| 41| 49|CCTAACCCT| 5| 5| 0|null| null|
+------+---------+-------+---------+--------+--------+-----------+----+-----+
only showing top 5 rows
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Last modified February 1, 2023: fix:race condition for local[n] in toCoverage method (#172) (a49c32b)