Customised calling of heterozygous snp
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
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skdutta2091 •
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I think vcf-annotate in vcftools command can filter out snps with less than four alternate alleles like this:
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.