.\" Manpage for QTLtools mbv.
.\" Contact halitongen@gmail.com to correct errors or typos.
.TH QTLtools-mbv 1 "06 May 2020" "QTLtools-v1.3" "Bioinformatics tools"
.SH NAME
QTLtools mbv \- Match genotypes in a VCF to a BAM file
.SH SYNOPSIS
.B QTLtools mbv \-\-bam [\fIsample.bam|sample.sam|sample.cram\fB] \-\-vcf [\fIin.vcf\fR|\fIin.bcf\fR|\fIin.vcf.gz\fB] \-\-out \fIoutput_file
[\fB\fIOPTIONS\fR]
.SH DESCRIPTION
This mode checks if the genotypes in the VCF are observed in the RNAseq reads in the BAM file to quickly solve sample mislabeling and detect cross-sample contamination and PCR amplification bias.
The details of the method are described <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6044394/>. 
In brief, we measure, for each individual in the VCF, the proportions of heterozygous and homozygous genotypes for which both alleles are captured by the sequencing reads in the BAM file. 
A 'match' would have close to 100% concordance for both measures, whereas a 'mismatch' will have significantly lower concordance for both metrics.
Increased cross-sample contaminations leads to decreased homozygous concordance values with no change in heterozygous concordance while increased amplification bias leads to decreased heterozygous concordance with no change in homozygous concordance.
We recommend using uniquely mapping reads only by specifying the correct \fB\-\-filter\-mapping\-quality\fR.
.SH OPTIONS
.TP
.B \-\-vcf [\fIin.vcf\fR|\fIin.bcf\fR|\fIin.vcf.gz\fB]
Genotypes in VCF/BCF format.
Should contain all the samples in the dataset.
REQUIRED. 
.TP
.B \-\-bam [\fIin.bam\fR|\fIin.sam\fR|\fIin.cram\fB]
Sequence data in BAM/SAM/CRAM format.
REQUIRED.
.TP
.B \-\-out \fIoutput\fR
Output file name
REQUIRED.
.TP
.B \-\-reg \fIchr:start-end\fR
Genomic region to be processed.
E.g. chr4:12334456-16334456, or chr5
.TP
.B \-\-filter\-mapping\-quality \fIinteger\fR
Minimum mapping quality for a read or read pair to be considered. 
Set this to only include uniquely mapped reads.
DEFAULT=10
.TP
.B \-\-filter\-base\-quality \fIinteger\fR
Minimum phred quality for a base to be considered. 
DEFAULT=5
.TP
.B \-\-filter\-binomial\-pvalue \fIfloat\fR
Binomial p-value threshold below which a heterozygous genotype is considered as exhibiting allelic imbalance. 
DEFAULT=0.05
.TP
.B \-\-filter\-minimal\-coverage \fIinteger\fR
Minimum number of reads overlapping a genotype for it to be considered. 
DEFAULT=10
.TP
.B \-\-filter\-imputation\-qual \fIfloat\fR
Minimum imputation information score for a variant to be considered. 
DEFAULT=0.9
.TP
.B \-\-filter\-imputation\-prob \fIfloat\fR
Minimum posterior probability for a genotype to be considered. 
DEFAULT=0.99
.TP
.B \-\-filter\-keep\-duplicates
Keep reads designated as duplicate by the aligner.



.SH OUTPUT FILE COLUMNS
.TP 1
.BI \-\-out " filename
This file does not have header and it contains the following columns:

.TS
n lx .
1	T{
The sample ID in the VCF against which the sequence data has been matched
T}
2	T{
The number of missing genotypes for this sample 
T}
3	T{
The total number of heterozygous genotypes examined
T}
4	T{
The total number of homozygous genotypes examined
T}
5	T{
The number of heterozygous genotypes considered for the matching, i.e. those that are covered by more than \fB\-\-filter\-minimal\-coverage\fR  
T}
6	T{
The number of homozygous genotypes considered for the matching, i.e. those that are covered by more than \fB\-\-filter\-minimal\-coverage\fR  
T}
7	T{
The number of heterozygous genotypes that match between this sample and the BAM file
T}
8	T{
The number of homozygous genotypes that match between this sample and the BAM file  
T}
9	T{
The percentage of heterozygous genotypes that match between this sample and the BAM file  
T}
10	T{
The percentage of homozygous genotypes that match between this sample and the BAM file  
T}
11	T{
The number of heterozygous genotypes with significant allelic imbalance  
T}
.TE

.SH EXAMPLES
.IP o 2
Running mbv on an RNAseq sample mapped with GEM:
.IP "" 2
QTLtools mbv \-\-bam HG00381.chr22.bam \-\-out HG00381.chr22.mbv.txt \-\-vcf genotypes.chr22.vcf.gz \-\-filter\-mapping\-quality 150
.sp
You can then plot column 9 vs. 10 to identify the genotyped sample in the VCF that matches best your sequence data.
.SH SEE ALSO
.IR QTLtools (1)
.\".IR QTLtools-bamstat (1),
.\".IR QTLtools-mbv (1),
.\".IR QTLtools-pca (1),
.\".IR QTLtools-correct (1),
.\".IR QTLtools-cis (1),
.\".IR QTLtools-trans (1),
.\".IR QTLtools-fenrich (1),
.\".IR QTLtools-fdensity (1),
.\".IR QTLtools-rtc (1),
.\".IR QTLtools-rtc-union (1),
.\".IR QTLtools-extract (1),
.\".IR QTLtools-quan (1),
.\".IR QTLtools-rep (1),
.\".IR QTLtools-gwas (1),
.PP
QTLtools website: <https://qtltools.github.io/qtltools>
.SH BUGS
Please submit bugs to <https://github.com/qtltools/qtltools>
.SH
CITATION
Fort A., Panousis N. I., Garieri M. et al. MBV: a method to solve sample mislabeling and detect technical bias in large combined genotype and sequencing assay datasets, \fIBioinformatics\fR \fB33\fR(12), 1895 2017.
<https://doi.org/10.1093/bioinformatics/btx074>
.SH AUTHORS
Olivier Delaneau (olivier.delaneau@gmail.com), Halit Ongen (halitongen@gmail.com)