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)