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7 votes
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Given a VCF of a human genome, how do I assess the quality against known SNVs?

To achieve (at least some of) your goals, I would recommend the Variant Effect Predictor (VEP). It is a flexible tool that provides several types of annotations on an input .vcf file. I agree that ...
  • 366
5 votes
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What are values of FILTER column of vcf files produced by Mutect2

You haven't told us what commands you ran, so I am assuming you first ran Mutect2 and then FilterMutectCalls. If so, the ...
  • 8,720
5 votes

Given a VCF of a human genome, how do I assess the quality against known SNVs?

The greatest protein coding variant catalogue is definitely ExAC (>65k individuals). They also published a blogpost where they describe how to reproduce figures in the paper (it is a good start how to ...
4 votes

Expected allele frequency distribution of SNVs in real NGS data

I don't have enough experience to answer which probabilistic distribution should be used. However, this questions also also asks how to estimate parameters of the distributions. If a binomial ...
  • 2,156
4 votes

Given a VCF of a human genome, how do I assess the quality against known SNVs?

Your best bet is to use programs that provide you an complete annotation of variants present in your VCF. Two examples are snpEff and Annovar. These programs work on known variants deem different ...
  • 182
3 votes
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Merging matched parts of two dataframes

If you have issue with memory and dealing with large object, maybe data.table is the way to go (https://github.com/Rdatatable/data.table/wiki): Let's take two ...
  • 1,021
2 votes

Help with the definitions of fields in a VCF output by Strelka

What is the difference of ReadCount in INFO column and DP in FORMAT column? I'm not super familiar with Strelka but I believe it follows the VCF spec, so DP in the FORMAT column should give the depth ...
1 vote

Merging matched parts of two dataframes

Read the manuals for data.table::merge and base::merge. This (wrong syntax): ...
  • 1,042
1 vote

Parsing .vcf file for this information

You can do the extraction part with the GATK tool VariantsToTable, as described here: https://gatk.broadinstitute.org/hc/en-us/articles/360041414592-VariantsToTable The usage example from that doc: ...
1 vote

Parsing .vcf file for this information

To extract the DP fields from a VCF file, you could use a tool like bcftools query: Extracts fields from VCF or BCF files and outputs them in user-defined format....

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