NAME

       QTLtools bamstat - Calculate stats of overlap between an RNAseq BAM file and an annotation

SYNOPSIS

       QTLtools bamstat --bam [sample.bam|sample.sam|sample.cram] --bed [gene_annotation.bed]  --out output_file
       [OPTIONS]

DESCRIPTION

       This  mode  counts  the  number  of  RNAseq reads, and the ones that overlap with an annotation file.  We
       recommend using uniquely mapping reads only by specifying the correct --filter-mapping-quality.

OPTIONS

       --bed  annotation.bed
              Annotation of interest REQUIRED.

       --bam, -b [in.bam|in.sam|in.cram]
              Sequence data in BAM/SAM/CRAM format.  REQUIRED.

       --out, -o output
              Output file name REQUIRED.

       --filter-mapping-quality integer
              Minimum mapping quality for a read or read pair to  be  considered.   Set  this  to  only  include
              uniquely mapped reads.  DEFAULT=10

       --filter-keep-duplicates
              Keep reads designated as duplicate by the aligner.  RECOMMENDED for RNAseq

OUTPUT FILE COLUMNS

       --out filename
        This file does not have header and it contains the following columns:

        1   The total number of reads in the BAM file
        2   The number of mapped sequencing reads passing the --filter-mapping-quality
        3   The number of mapped sequencing reads falling within the annotations specified with --bed
        4   The total number of annotations in the --bed file
        5   The number of annotations covered by at least one sequencing read

EXAMPLES

       o Running bamstat on an RNAseq sample mapped with GEM and GENCODE gene annotations:

         QTLtools     bamstat     --bam     HG00381.chr22.bam      --out     HG00381.chr22.bamstat.txt     --bed
         gencode.v19.annotation.bed.gz --filter-mapping-quality 150 --filter-keep-duplicates

SEE ALSO

       QTLtools(1)

       QTLtools website: <https://qtltools.github.io/qtltools>

BUGS

       Please submit bugs to <https://github.com/qtltools/qtltools>

CITATION

       Delaneau, O., Ongen, H., Brown, A. et al. A complete tool set for molecular QTL discovery  and  analysis.
       Nat Commun 8, 15452 (2017).  <https://doi.org/10.1038/ncomms15452>

AUTHORS

       Olivier Delaneau (olivier.delaneau@gmail.com), Halit Ongen (halitongen@gmail.com)

QTLtools-v1.3                                      06 May 2020                               QTLtools-bamstat(1)