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Interpretation of SNP Analysis

After generating individual vcf files in both control and disease group, How we can interpret about disease SNP? because some SNPs were common in Control and Disease group.

snp
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updated by h.mon h.mon • written by rebecca08238 • rebecca08238

1 answer

Some remarks:

  1. this forum is more geared towards the technical aspects of bioinformatics analysis, not helping in (complex) interpretation of analysis results;

  2. your question has no details about methods used, sample size, experimental design, the nature of the disease you are interested in, and so on, so it is impossible to help with your results interpretation, even if one wishes to help with that;

Designing studies to pinpoint mutations responsible for diseases and interpreting their results is a difficult task, and one I am no expert at. I enjoy reading, and learn a lot from, the blog Kids genomics - it will provide you with ample references to help you in having a better grasp of the problem.

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written by h.mon h.mon

Thanks for your reply, My work flow: After getting raw data from Illumina Miseq. (Illumina Ampliseq kit was used ) (Source: genomic DNA) reference genome used: hg19 (I used samtool pipeline) 1st step: Mapping was done by using BWA mem 2nd step: Conversion of Sam to Bam file (using a fixmate command) 3rd step Bam sorting& Bam indexing 4th step: Variant calling using bcftools (v1.9) we created 2 groups files: group1 Normal 30 Individuals and group 2: syndromic patients total 60 individuals in second group. Is this a correct way to generate vcf files or we have to make vcf files for each sample of a particular group and then combining all samples groupwise? So now we have two vcf files: group1.vcf & group2.vcf, I used SnpEff for annotation of these two groups files. I observed that some of the SNPs are present in the control group and syndromic group too, So should I remove those SNPs which are common in both groups using bedtools subtract command?

Even I also generate individual patients(30 control &60 syndromic patients) vcf files and annotate it individually...After this I am stuck, not getting an idea what to do next actually I want to check SNP which are link with syndromic group. After generating individually 30 controls samples vcf and 60 syndromic one so now I want to combine all control in one vcf file and all syndromic group in one vcf file, I tried with vcf isec command but I took only a few SNPs not .... So can you plz let me know the command to combine these files?

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written by rebecca08238 • rebecca08238

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