I have bam files of WXS and I'm visualizing it with IGV. Can I genotype a SNP only by visualizing its reads and bases in IGV? Are there any standard? Like minimum coverage or a threshould to call heterozygous (20%? 30%?).
Example: In some snp, in igv, I have a 20x coverage for that position and 20% of C and 80% of T (observing homogeneous distribution in both strands) . Can I call this a CT?
Are there any other way to call a genotype of a SNP in NGS data (bam) other than variant caller? I did that, but some of my snps are not being called in VCF file.
There is no standard for this, and performing this manual inspection requires experience more than anything else. However, as I recently did this for a private company in New York, USA, I can share my own experience.
That of which to be aware:
overall read depth over the variant position. For a germline variant, technically, my work from the clinical setting in the NHS England shows that 18 is the bare minimum that one should want, with 30 being ideal.
read bias - is the variant mostly called in R1 or R2?
position bias - is the variant called at the end of reads?
quality of reads - are the reads flagged in IGV for any reason?
MAPQ of the reads
are there many base-mismatches in the reads aligning to the general region surrounding the variant, and/or indels with a seemingly sporadic / random distribution?
is it a repeat region, or do any reads span a repeat region by even a few bases?
