EstimatePoolingFractions

Overview

Group: SAM/BAM

Examines sequence data generated from a pooled sample and estimates the fraction of sequence data coming from each constituent sample. Uses a VCF of known genotypes for the samples within the mixture along with a BAM of sequencing data derived from the pool. Performs a multiple regression for the alternative allele fractions at each SNP locus, using as inputs the individual sample’s genotypes. Only SNPs that are bi-allelic within the pooled samples are used.

Each sample’s contribution of REF vs. ALT alleles at each site is derived in one of two ways: (1) if the sample’s genotype in the VCF has the AF attribute then the value from that field will be used, (2) if the genotype has no AF attribute then the contribution is estimated based on the genotype (e.g. 0/0 will be 100% ref, 0/1 will be 50% ref and 50% alt, etc.).

Various filtering parameters can be used to control which loci are used:

–intervals will restrict analysis to variants within the described intervals
–min-genotype-quality will filter out any site with any genotype with GQ < n
–min-mean-sample-coverage requires that the coverage of a site in the BAM be >= min-mean-sample-coverage * n_samples
–min-mapping-quality filters out reads in the BAM with MQ < n
–min-base-quality filters out bases in the BAM with Q < n

Arguments

Name	Flag	Type	Description	Required?	Max # of Values	Default Value(s)
vcf	v	PathToVcf	VCF of individual sample genotypes.	Required	1
bam	b	PathToBam	Path to BAM file of sequencing data.	Required	1
output	o	FilePath	Output file to write with pooling fractions.	Required	1
intervals	l	PathToIntervals	Zero or more set of regions to restrict analysis to.	Optional	Unlimited
samples	s	String	Optional subset of samples from VCF to use.	Optional	Unlimited
non-autosomes	n	String	Non-autosomal chromosomes to avoid.	Required	Unlimited	M, chrM, MT, X, chrX, Y, chrY
min-genotype-quality	g	Int	Minimum genotype quality. Use -1 to disable.	Optional	1	30
min-mean-sample-coverage	c	Int	Minimum (sequencing coverage @ SNP site / n_samples).	Optional	1	6
min-mapping-quality	m	Int	Minimum mapping quality.	Optional	1	20
min-base-quality	q	Int	Minimum base quality.	Optional	1	5