BamQC¶

Contents:

Created on 12 Oct 2016

@author: ernesto

class BamQC.BamQC.BamQC(bam, samtools_folder=None, java_folder=None, picard_folder=None, chk_indel_folder=None, verifybamid_folder=None)¶

Class to do the quality assessment on a BAM format file

Methods

`aggregate_stats`(cov_list)	Used to calculate aggregated stats on a list of SDepth objects
`get_contigs`()	Get all contigs from this BAM
`get_simple_stats`()	Get a dict with stats on the BAM file as calculated by samtools flagstat
`list_of_readgroups`()	Get the Read Groups extracted from the header of the BAM file
`list_of_samples`()	Get the samples names from the header of the BAM file
`run_CollectHsMetrics`(baits_file[, outfile, …])	Run Picard’s CollectHsMetrics on a Exome sequencing BAM file
`run_CollectWgsMetrics`(reference[, outfile, …])	Run Picard’s CollectWgsMetrics on a WGS BAM file
`run_chk_indel_rg`([outfile])	Run Heng Li’s chk_indel_rg on a BAM file
`run_samtools_depth`(chros)	Calculate several coverage metrics on a whole genome sequencing BAM file using ‘samtools depth’
`run_verifybamid`(genotype_file, outprefix[, …])	Run VerifyBAMID to check for sample swap or contamination issues

aggregate_stats(cov_list)¶

Used to calculate aggregated stats on a list of SDepth objects

Parameters:	cov_list : list List containing the SDepth objects for which the stats will be aggregated.
Returns:	A SDepth object

get_contigs()¶

Get all contigs from this BAM

Parameters:	None
Returns:	dict A dictionary containing the following information: {‘contig Name’: length (in bp)}

get_simple_stats()¶

Get a dict with stats on the BAM file as calculated by samtools flagstat

Parameters:	None
Returns:	dict A dictionary containing the following information: { “total_no_reads”: int “no_duplicates”: int “total_no_mapped”: int “no_properly_paired”: int }

list_of_readgroups()¶

Get the Read Groups extracted from the header of the BAM file

Parameters:	None
Returns:	list List composed of the read groups

list_of_samples()¶

Get the samples names from the header of the BAM file

Parameters:	None
Returns:	list List with the sample names

run_CollectHsMetrics(baits_file, outfile=None, cov_cap=None)¶

Run Picard’s CollectHsMetrics on a Exome sequencing BAM file

Parameters:	baits_file : filename Path to the file containing the Exome baits. outfile : filename, optional If provided, then create a file with the output of this program cov_cap : int, optional Picard’s Coverage Cap parameter. Treat positions with coverage exceeding this value as if they had coverage at this value. Default value: 250. Returns —— A CMetrics object

run_CollectWgsMetrics(reference, outfile=None, cov_cap=None)¶

Run Picard’s CollectWgsMetrics on a WGS BAM file

Parameters:	reference : filename Fasta file used as the genome reference outfile : filename, optional If provided, then create a file with the output of this program cov_cap : int, optional Picard’s Coverage Cap parameter. Treat positions with coverage exceeding this value as if they had coverage at this value. Default value: 250. Returns —— A CMetrics object

run_chk_indel_rg(outfile=None)¶

Run Heng Li’s chk_indel_rg on a BAM file

Parameters:	outfile : filename, optional If provided, then create a file with the output of this program
Returns:	list A list of Chk_indel objects

run_samtools_depth(chros)¶

Calculate several coverage metrics on a whole genome sequencing BAM file using ‘samtools depth’

Parameters:

chros : list or string

List of contigs or just a single contig used for calculating the coverage

Returns

——

List of SDepth objects

This method runs samtools depth on a BAM file and will calculate the following metrics:

Number of Bases mapped: This is the number of bases having at least one read mapped
Sum of depths of coverage: This is the sum of all the depths in each of the Bases mapped
Breadth of coverage: This is the result of dividing bases_mapped/length(contig) (i.e. what portion of the contig has reads mapped)
Depth of coverage: This is the result of dividing sum_of_depths/length(contig)

run_verifybamid(genotype_file, outprefix, outdir=None)¶

Run VerifyBAMID to check for sample swap or contamination issues

Parameters:	genotype_file : filename vcf file with chip genotypes to use outprefix : str prefix for outputfiles outdir : str, optional If provided, then put output files in this folder
Returns:	list A list with the paths to the output files generated by VerifyBAMID

class BamQC.BamQC.CMetrics(metrics, cov_data)¶

Class to store coverage information on the metrics calculated by Picard’s CollectHsMetrics/CollectWgsMetrics on an Exome or WGS BAM file

Methods

`create_cov_barplot`(filename[, xlim, ylim])	This method will create a Barplot using the different coverage values counts calculated by Picard’s CollectHsMetrics or CollectWgsMetrics
`print_report`([filename])	Used to print a text report of data in the object

create_cov_barplot(filename, xlim=None, ylim=None)¶

This method will create a Barplot using the different coverage values counts calculated by Picard’s CollectHsMetrics or CollectWgsMetrics

Parameters:	filename : filename PDF file to write the plot. xlim : tuple, optional Set the X-axis limit ylim : tuple, optional Set the Y-axis limit

print_report(filename=None)¶

Used to print a text report of data in the object

Parameters:	filename : filename, optional Filename to write the report. The default is STDOUT.

class BamQC.BamQC.Chk_indel(RG, ins_in_short_homopolymer, del_in_short, ins_in_long, del_in_long, outcome=None)¶

Class to store information on the ratio of short insertion and deletion calculated by runnint Heng Li’s chk_indel_rg

Methods

calc_ratio() Method to calc ratio ins-in-short-homopolymer/del-in-short and check if it is > 5

calc_ratio()¶

Method to calc ratio ins-in-short-homopolymer/del-in-short and check if it is > 5

Returns:	str It returns PASS/FAILED depending on the outcome of the test

class BamQC.BamQC.SDepth(contig=None, mapped=None, breadth=None, depth=None, length=None, sum_of_depths=None, max=None)¶

Class to store coverage metrics on a Whole Genome Sequencing BAM file calculated using SAMtools depth

Methods

print_report([filename]) Used to print a text report of data in the object

print_report(filename=None)¶

Used to print a text report of data in the object

Parameters:	filename : filename, optional Filename used to write the report. The default is STDOUT.