how can I write a script for calculate snp variants coverage

Question

[bioinfonewbie]

hello everyone, im new in coding areas and I have a question. I have a bedfile for a complex disease(example obesity, type 2 diabetes) releated snp variants and I have another file for 10 people genome data. I want to calculate my variants 10kb arounds genome coverage for this 10 people genome data. My language is not okey, I know that but I hope you all understand my problem. For this problem I want to write a script for linux but I don't know where to start or what to do. Thanks for helping.

Answer 1

[ATpoint]

Your english is totally fine, don't worry. As for the question, the problem is that you have to consider the alignment quality, base quality and the actual reference base to decide whether a read reliably indicates a variant at a given position. I would therefore probably run your 10 people through a variant calling pipeline, e.g. GATK (or at best the variant caller that was used to come up with this BED file) and then intersect the resulting VCF files with the BED file. Does that make sense in your case? In which format do you have your data? Something like BAM or fastq?

[bioinfonewbie]

its bam file, actually they are ancient people form different ages. I want tto understand if that person carries variants that increase the likelihood of the disease occurring. my bed file is look like this , ı also look my variants chromosome positions 10kb around. chr start end chr1 219465882 219475882 chr1 65508597 65518597 chr1 177878445 177888445 chr1 72367846 72377846 chr1 72280502 72290502 chr1 72294433 72304433 chr1 177914890 177924890 chr2 626183 636183 . . .

[ATpoint]

Ok, then as said, run them through a variant caller and intersect them with the BED files. The VCF contains depth for REF and ALT.

[bioinfonewbie]

thanks al lot for helping !