I am trying different things in Samtools to get a reasonable .vcf file for 2 human exomes I have sequenced.
Whatever I do I keep getting a file of ~600Mb which has millions of rows and can't fully open in Excel. I would expect ~22,000 variant calls per person so I assume this file is filled with sequencing blips that aren't genuine variants.
The method I have tried are making a pileup and converting a bcf to vcf via the varFilter command:
samtools mpileup -g -f hg19.fa aln.srt.bam > raw.bcf
bcftools view -vcg raw.bcf > var.bcf
bcftools view var.bcf | perl vcfutils.pl varFilter > var-final.vcf
I have also tried this:
samtools mpileup -uf hg19.fa srt.bam | bcftools call -mv - > file.vcf
Can anyone tell me how to best call rare variants in Samtools?