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Old 12-20-2011, 11:16 PM   #1
Location: Bonn

Join Date: Feb 2010
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Default A heretically simple approach to variant calling

Hi everyone,

we had a look at the distribution of heterozygous allele frequencies in NGS datasets and found that their variance is larger than expected by a bionomial distribution ( For every variant caller this means a binomial prior distribution is not the right choice and might lead to false negative calls. We also found that a simple frequency classifier (heterozygous if covered by more the 20 reads and variant allele between 14% and 86%) is more sensitive at comparable specificity for high quality data, compared to default setting of most standard calling tools.

Is anyone aware of a fast tool, that allows to apply such a frequency filter directly on a .bam file?


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Old 12-21-2011, 02:58 AM   #2
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You can ask samtools mpileup to print out the nucleotide pileups for each position in bam file. Parsing that should be fairly simple with a script.
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Old 02-04-2012, 04:07 AM   #3
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the samtools mpileup output can be piped into VarScan to apply a coverage and frequency filter:
samtools pileup -f reference.fasta myData.bam | java -jar VarScan.v2.2.jar pileup2snp --min-coverage 20 --min-var-freq 0.14
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Old 04-24-2012, 08:10 AM   #4
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Very nice paper.

Sometimes simpler is better.
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Old 04-25-2012, 03:01 AM   #5
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This is awesome. Moving away from big fancy well-established tools to something like the "14-86%" rule is scary though.
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allele distributions, variant calling

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