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Old 07-31-2018, 08:59 PM   #1
Chen-Tau Lin
Junior Member
 
Location: Republic of Taiwan

Join Date: Jul 2018
Posts: 1
Default The R-square between coverage and short variants number

Hello, everyone

I've called variants with 3 kinds of short variants caller to decide which one to use for calling variants.

I generate a dot plot with coverage for X and SNP numbers for Y to see if the coverage impact the number of short variants.

The average coverage of my 40 birds is 15.4 +-2
I've called short variants from my 40 bam files which do recalibration 2 times with
GATK 3.7 UnifiedGenotyper
GATK 4.0 HaplotypeCaller
Samtools mpileup which short variants is cut off with two times and one third the coverage of each sample

I think the R-square is the lower the better, because the actual short variants number should not have high relation with called coverage.

Does anyone have other opinion ?
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coverage depth, variance calling

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