How to filter SNP and Indel under these criteria?

Question

[r00628112]

Genome-wide polymorphism analysis: after using freebayes to identify SNP and Indel, I will follow these criteria for filtering: (1) the minimum variant frequency of ≥ 90%, (2)average quality of the SNP base ≥ 30 and minimum read depth of 10.

Question1: what kind the tools can be used for these criteria filtering?

Question2: After variation filtering, I'm curious about how to compare the SNPs/Indel difference between cultivars? I analyzed re-sequencing data between four cultivars.

For example, there are A, B, C and D cultivars in the vcf file. But I would like to compare the SNP/Indel variance between A/B and A/C (such as SNP/Indel number)

Thank you very much

[jared.andrews07]

bcftools can be used for filtering (on nearly any criteria). Your second question could use some clarification. Do you want to compare allele frequencies between the different cultivars? Or just whether variants were called/not called between each?

[r00628112]

Thanks to your suggestion. Because of limited data, I would like follow this paper to do the analysis of Genome-wide DNA polymorphisms by using four cultivars re-sequencing data. I would like make this kind of table and picture in this paper, thus I'm curious about how to comparing the SNP or Indel number between two cultivars in a combined VCF file. https://www.nature.com/articles/s41598-018-32513-z/tables/2 https://www.nature.com/articles/s41598-018-32513-z/figures/1

Answer 1

[tothepoint]

You may try GATK filtering and check if this help.

gatk SelectVariants -V vcffile.vcf.gz -select-type SNP -O snps.vcf.gz

gatk SelectVariants -V vcffile.vcf.gz -select-type INDEL -O indels.vcf.gz