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Old 08-17-2011, 04:42 PM   #4
Richard Finney
Senior Member
Location: bethesda

Join Date: Feb 2009
Posts: 699

You can force samtools mpileup with pipe to bcftools to produce lots'o'info like this ...

samtools mpileup -R -d 1000 -l rangehg18.chr -uf hg18.fa in.bam | bcftools view -g - > out.vcf

Note the -g parameter, it forces calls and outputs for all locations.
Check why you're not getting calls in the details of the VCF file.
You can write your own caller based on the VCF information if you need to.
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