co-occurrence matrix from my VCF file

Question

[HarperReed]

Hello, I'm working with a haploid organism and want to build a co-occurrence matrix from my VCF file to identify which variants/mutations co-occur on the same read. When I worked with diploid organisms, I had to phase the VCF file before constructing this matrix. Now that I'm focusing on a haploid organism, what should I do? Can I still use the same logic of phasing (even though it's haploid), or is there a different approach I should take to build the matrix?

thank you in advance

Answer 1

[robben]

From the VCF designation https://samtools.github.io/hts-specs/VCFv4.2.pdf

Each row represents a new variant but because multiple reads are used to call variants it no longer has the information at the read level. It does however have positional information so you can likely use that to look in you BAM/SAM file for reads that span multiple variants. Some psuedocode might be:

for row in SAM:
for row in VCF:
    if SAM.start < VCF.position { Left = VCF.row }
    if SAM.end > VCF.position { Right = VCF.row }
done
if Left & Right { contains2 = True }
Spanning[row,] = [contains2, Left, Right]

Also, it shouldn't be a problem with the phasing because a single read is physically incapable of having sequence from both genomes of a diploid organisms since each read is from a single DNA molecule.