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very different SNP calling by GATK and samtools

ymwymw Member Posts: 13
edited February 2013 in Ask the GATK team

I am estimating SNP number for a genome of a speceis.

  1. After mapping the illumina reads to a reference seqence (of a related species), I used picard to remove duplicates and used samtools (mpileup) to convert the bam file to a fastq file.
  2. I also use GATK to do local reglimant and recalication from the mappnig bam file. Then I used samtools (mpileup) to convert the bam files output by GATK to a fastq file.

I found that the number of SNP in the fastq going through GATK is 10 times more than the first fastq.
Interestingly, if I use picard to do duplicats-removomg again to the GATK bam and used samtools to convert the bam to fastq file. The SNP jumps back to 10 time fewer.

What can be the reason that the SNP number can be 10 time different between the two methods?
Actually, I expect the GATK output file has fewer SNP given the effect of recaliraiton or relingement. But the result is opposite.


Post edited by Geraldine_VdAuwera on


  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 11,130 admin

    Hi Chih-Ming,

    This is not really surprising, as the GATK variant callers (UnifiedGenotyper and HaplotypeCaller) are intentionally designed to be very permissive in calling variants. The key step is Variant Quality Score Recalibration, which uses the annotation metrics to distinguish real variants from noise. The earlier processing steps such as base recalibration and alignment are used to improve the reliability of those annotations. So what you should compare is the number of variants after VQSR.

    Geraldine Van der Auwera, PhD

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