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How to run bamstat?

The bamstat mode of QTLtools requires two files as input:

• A BAM file containing the sequence data of a molecular assay.
• A BED file containing the reference annotation for this molecular assay

To illustrate how it works, we provide the 2 following example files:

• A RNA-seq BAM file on chr22 for sample HG00381: BAM / index
• An annotation BED file on chr22 derived from GENCODEv19: link

Then, you can run bamstat on these two files running the command:

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

Note that we use the option --filter-mapping-quality 150 since it is the recommended value to remove bad quality reads in a BAM generated with the GEM mapper.

This command produces an output file HG00381.chr22.bamstat.txt as follows:

610860 489276 469678 26771 20179

The 5 columns give:

• A. The total number of sequencing reads in the BAM file (=610,860)
• B. The number of mapped sequencing reads passing the --filter-mapping-quality filter (=489,276)
• C. The number of mapped sequencing reads falling within the annotations specified with --bed (=469,678)
• D. The total number of annotations in the --bed file (=26,771)
• E. The number of annotations covered by at least one sequencing read (=20,179)

From this file, you can then compute the ratios B/A=80%, C/A=77% or E/D=75% to assess the quality of your sequence data.