I am aiming to extract the full information at each site: read depth, # ref reads, # variant reads (for all non-reference alleles), strand information, etc. An old thread started by nilmot13 suggested "genomeCoverageBed", but the output seems to contain only simple read depth.
My problem started from an observation that SAMtools and GATK generate very different REF/ALT read depth at some site from the same BAM file, while BAMview and IGV both tend to support GATK counts at the site.
My problem started from an observation that SAMtools and GATK generate very different REF/ALT read depth at some site from the same BAM file, while BAMview and IGV both tend to support GATK counts at the site.
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