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Old 12-06-2011, 08:01 AM   #1
Location: Ospedali Riuniti di Bergamo, ITALY

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Default minimum depth variant calling samtools/gatk

Hi NGS user,
does anyone know how I can set a minimum coverage threshold in variant calling in samtools mpileup and in GATK Unified Genotyper. I only find parameter to set max per-BAM depth to avoid excessive memory usage.

Thanks a lot,
m_elena_bioinfo is offline   Reply With Quote
Old 12-06-2011, 08:31 AM   #2
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Location: St. Louis

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With SAMtools you can filter out calls under X coverage using:

/samtools-0.1.18/bcftools/ varFilter -d X <input.vcf> > <output.vcf>
Heisman is offline   Reply With Quote

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