What are good settings for filtering VCF files?
1
8
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7.1 years ago
devenvyas ▴ 680

I followed the samtools/bcfutils/vcfutils pathway followed here http://ged.msu.edu/angus/tutorials-2012/snp_tutorial.html to convert a set of human Hg19-aligned BAM files into a set of raw VCF files. I then got vcftools to filter down to just autosomal SNPs. These are really, really, really low-coverage genomes (they were enriched for NRY and/or mtDNA, and I am just trying to make use of the "leftovers")

Now I have the data I want, but I am trying to found out what of it is actually useable. I was wondering what are good filtering parameters for tossing/keeping human SNPs (or where can I find said parameters)? Thanks!

-Deven

 

vcftools samtools SNP bcftools • 15k views
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7.1 years ago

This is what I use. I generally change them depending on the study. But more or less this is close to what everyone uses. 

MinDP (Minimum read depth):   5 (Indels) and 3 (SNPs)
MaxDP (Maximum read depth):  You have a low coverage data, so I would set it to 100. Normally it is 3 times the average coverage.
BaseQualBias (Minimum p-value for baseQ bias):  0
MinMQ (Minimum RMS mapping quality for SNPs):  20 or 30 (to be more stringent)
Qual (Minimum value of QUAL field):  15 or 20

StrandBias (Minimum p-value for strand bias):  0.0001
EndDistBias (Minimum p-value for end distance bias):  0.0001
MapQualBias (Minimum p-value for mapQ bias):  0
VBD (Minimum Variant Distance Bias):  0 (More relevant to RNA-seq reads)

GapWin (Window size for filtering adjacent gaps):  30 bp
SnpGap (SNP within INT bp around a gap to be filtered):   20 bp

SNPcluster (number of snps within a region): I usually drop all the snps if there are more than 3 snps within 10 bp. 

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@Ashutosh -

could you provide reasoning as to why those are the thresholds you typically use? It would be helpful so researchers can understand the parameters better! Thanks!

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You are right to question this - indeed, there are absolutely no standards for these filtering criteria. Take a look at my take on DP alone: A: DP in VCF files?

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I know vcftools can filter based on DP/Qual, do you have any recommendations on what to use to do the other filtering? Thanks!

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This one does almost everything that's mentioned above.
 

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I have my own python script. If you know python you can modify it for your use. (https://github.com/ashutoshkpandey/Variants_call/blob/master/Filter_samtools_vcf.py)  OR you can use vcf-tools  "annotate" feature.  I think the second option will be much better. 

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