Customised calling of heterozygous snp

Question

[skdutta2091]

Dear friends,

I have a vcf file containing only snps (indels are removed) with a depth read of 15. I want to set a criteria to find heterozygous snp from that vcf file where a particular alternate allele is present in atleast 4 reads among the 15 reads or more in the alignment file (.bam).

Can anybody please tell me whether I need to script for this or not? Or are there any in built tools in vcftools for this kind of customised snp calling?

Regards

[mkulecka]

I think vcf-annotate in vcftools command can filter out snps with less than four alternate alleles like this:

cat your.vcf | vcf-annotate -r FILTER/MinAB 4 | grep -E "#|PASS" > filtered.vcf

However, I think you are better off re-calling variants in bam files with changed parameters in your variant caller - most callers have options of adjusting minimum number of alternate bases.