Compare ID SNP variants across samples
The ID SNP variants track can be used to assess whether different samples are from the same patient, as described below. Note that only ID SNP positions where the detected variant is different from the reference genome are included in this track.
- Generate a graph track for each sample from the read mapping using Create Mapping Graph with only the "Paired read specific coverage" option checked.
- Detect regions of low coverage in each sample using Identify Graph Threshold Areas with the "Use upper threshold" option checked.
- Combine the identified low coverage regions using Merge Annotation Tracks.
- Exclude SNPs located in low coverage regions for each sample using Filter Based on Overlap with the "Remove overlapping annotations" option selected.
- Compare ID SNPs between samples using Identify Shared Variants. The output will include a "Sample count" attribute indicating how many samples contain each SNP.
- Retain only the ID SNPs not present in all samples using Filter on Custom Criteria with the filter criterion "Sample count < n", where n is the number of samples (typically 2).
The output will contain only the ID SNPs that differ between the samples. Based on this, the degree of similarity between the samples can be evaluated, to assess if they are likely to originate from the same patient.