find snp depth and total depth

Question

[paumarc]

Hi

I have a fastq file with segments of dna coming from different patients (DNA where mixed before being sequenced, so I expect to find different snp in a single position. i would like to find the total depth for the position , which i can do using samtools depth, and the depth for each snp (number the times that each variant appears at each position). I was looking at the DP fields of the vcf file but it seems not enough reads. Can any body tell me how i can compute the number of reads for each snp?

thanks

[cpad0112]

DP in info field is overall read depth for that SNP and DP in format field is sample read depth. Compare DP from VCF with those from bam. If they match, then your VCF is correct. If they do not, look at your variant calling parameters.

[paumarc]

thanks for your answer. Now my question is: if my dp field at the vcf is 6, does it means that i have only 6 reads or 600 or what? i think 6 reads is a low number for the experiment

p

[cpad0112]

If DP is 6 in INFO field, then overall read depth is 6. If DP in format field is 6, then your sample has read depth of 6. Load bam and VCF files in IGV and manually inspect the read depth for a few SNVs. In general, there is a quality filtering and several other parameters that are used in variant calling.