dear all, i am using samtool, bcf tool and vcf tools for variant calling of hexaploidy plant data which is sequenced by illumina hiseq 1000 and read length is 83 bp.this is paired end data. and also using snpEff for variant filter from vcf file by different parameter like QUAL>30 and DP > 10. 1- samtools for calling all variant 2- bcftools for only view genotype variants 3- snpEff for filter genotypic variant based on variant depth DP>10 and variant base quality QUAL >30 and remove other below on this parameter. 4- vcf tools for count variation like SNP and INdel.
So i want ask to all what is the standard parameter for filter true SNP and indel? whatever i used for true SNP is ok or need to change something? thank you..