Hello! I am working on Nephrotic syndrome patients. I have to check SNPs which are link with Nephrotic syndrome. study Involves 2 groups: Control, Nephrotic syndrome
Work done till now:
We used DNA Ampliseq illumina Library kit.
Let me tell you in brief what I did after getting raw data from Illumina Miseq. We used samtool pipeline
- Reference genome used: hg19
- 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: Control 30 individuals and group 2: syndromic patients total 60 individuals in second group.We used BCF isec command, 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? Please let me know that I am going in a proper way or not.
- Even I tried to create individual patients vcf files total 90 Samples (30 control and 60 syndromic. But after this I am stuck what to do. I used bcf isec command to combine all snp of 1 group into single vcf file but it’s taking only few SNPs my why it’s like that? Can you please help me which command I should use to combine all snp of one group.
- Can you please let me know If you had any idea that how we can say that this or that particular SNP responsible for particular disease.
Thank you !