I have 30 samples to call SNPs against same reference. All samples were aligned to reference using bowtie2 to get separate sam files. Those were used in calling.
What is the best way to call SNP and filter:
-- Call SNP together like:
samtools mpileup -uf genome.fa sam1.bam sam2.bam ....sam30.bam | bcftools view -I -bvcg -> all30.bcf bcftools view all30.bcf | vcfutils.pl varFilter -d 10 > all30.vcf
I found that even without any read coverage vcf file had genotype exactly as in reference if one of the sample had SNP in that particular location.
If there is SNP, I want coverage in all samples or maybe 1 missing.
29 samples should have coverage of 10 and if Het: minor allele frequency of 30% (i.e 3).
Thanks in advace.