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In Strelka vcf in INFO column we have these

Depth="The number of reads covering the variant position including duplicates, supplementary records and reads that fall below minimum base and mapping quality thresholds."

ReadCount="The number of reads covering the variant position excluding duplicates, supplementary records and reads that fall below minimum base and mapping quality thresholds.">
ReadCountControl="The number of reads covering the variant position in the control excluding duplicates, supplementary records and reads that fall below minimum base and mapping quality thresholds.">

And in FORMAT column we have

AU="Number of 'A' alleles used in tiers 1,2">
CU="Number of 'C' alleles used in tiers 1,2">
DP="Read depth for tier1 (used+filtered)">
GU="Number of 'G' alleles used in tiers 1,2">
TU="Number of 'T' alleles used in tiers 1,2">

What is the difference of ReadCount in INFO column and DP in FORMAT column?

What is the difference of number of allele versus number of reads covering the variant position ?

Please help for clarification if you have any intuition on this definitions

Thanks

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  • $\begingroup$ Can you post a small sample of your vcf file so we can have a look? My guess is that perhaps the DP/FORMAT field gives the total number of reads for all individuals in that particular SNP. But it's hard to say without seeing the rest of the vcf file. $\endgroup$ – user438383 Feb 28 at 13:23
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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 of coverage (ie read count) per sample. ReadCount in INFO is not in the VCF spec but based on the definition it sounds like the depth of coverage aggregated over all samples.

What is the difference of number of allele versus number of reads covering the variant position ?

I believe the "number of alleles used" refers to counts of each base that are used in the indel error modeling process as described in the preprint here:

https://www.biorxiv.org/content/10.1101/192872v2.full

So it sounds like subsets of the number of reads covering the variant position.

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