Question regarding MetaSNV

[kaysahu]

Hi,
Questions regarding MetaSNV compilation and output files.

1. What is the format/meaning of each column in the snpCaller folder?
   

2. In the snpCaller folder, the first piece is processed but the rest of them are empty. Can you please shed some light on why is that?

3. Is it normal to have empty folders/files in the output directory after post-processing?
   

Kindly let me know if anything is required from my side. Thanks.

[CosteaPaul]

Hey there,

So, let's start with the beginning.
Col1: contig id
Col2: i genuenly don't remember. if important, i can look it up.
Col3: position on contig
Col4: reference base
Col5: total coverage over base
Col6: coma separated SNP information. each representing: SNP_count | SNP_base | codon change (if you provided a genes location file) | cov sum

I'm not sure i follow what you mean by the second question, please elaborate.

On the last one, yes, it's perfectly fine for the indiv files to be empty. The joining of the called and indiv will always be the same, but different SNPs will end up in a different file based on some of the parameters, like the min frequency cutoff. So, if a SNPs is very low frequency in the population you are considering, I call it an individual SNP and thus will end up in the respective file.

Cheers,
-Paul

[kaysahu]

Hi Paul,

Thank you for your response. Here some follow up questions I have :

1. For the indiv files, it looks5like the program stopped in the middle and cannot finish the filtering steps. Would you happen to know why/any steps to rectify this.
2. From the contig info, pos 3,4,5 are not 'N' as we checked in the files. However, MetaSNV results show it is N in col 3. I am confused as to how this is possible.
3. Why is the reference base 'N' when we check the contig file and it is not N. This is an extension of question 2.

Looking forward to hearing from you.

[kaysahu]

Hi Paul,

Following up on my previous post since I haven't heard from you. Kindly let me know if my questions need any clarification. Looking forward to hearing from you.

[alimayy]

@kaysahu , @CosteaPaul , see metasnv-tool/metaSNV#3