SNP downstream analysis

Question

[aabhordia]

I have annotated SNPs using SnpEff and got files in HTML and CSV format. Could anyone please tell me now what further steps should I performed for further downstream analysis. I am new to this field any help would be great. Thank you in advance

Answer 1

[abedkurdi10]

you can compare the VCF files of different conditions: you can check for the common mutations between the conditions you are studying, you can check for the unique mutations for each group...

Answer 2

[Prash]

You could use bcftools filter followed by awk/sed liners. Before you start this,w hat would be your question? what are the inherent sample specifics you are looking into? For example, if you want to have a cutoff for depth, please use the following for depth 20 cutoff bcftools filter -i 'MIN(INFO/DP)>20' filename.vcf > filename_output_DP20.vcf

This could be followed by looking into hom/het calls etc.

The same could also be deployed for csv files as well.

Hope this helps

Answer 3

[aabhordia]

do I have to analyse vcf population-wise and compare the vcf files of each population for estimating genetic diversity????? And as I have mentioned that I have annotated vcf file that means I had to do further analysis using this annotated file only???

please suggest me how to proceed further. Thank you in advance

[abedkurdi10]

Your analysis depends on what are you looking for. Are you looking for mutations in specific genes? Are you looking for specific mutations in specific genes? Are you looking for novel mutations?

[aabhordia]

I am actually looking for variations affecting population present in different locations