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 ?
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 ?