How to make snp calling with GATK under the same depth come true?

Question

[zhengyunchaosky]

Recently I have dealt with 10 samples of rice genome resequencing. To control the results for comparison, I think it's better to do SNP calling under the same practical average depth. However, I couldn't get the same depth though I used 50X sequencing to all the samples. Is it possible to come true? How?

Answer 1

[h.mon]

Perform the variant calling the usual way and then filter the VCF file for minimum and maximum read depth (and other filter of choice). See here, here and here for some discussions on appropriate filters, you can easily find many more.

Answer 2

[zhengyunchaosky]

Many thanks for your respond!! really helpful!!