How to use samtools/bcftoos/vcfutils to call SNP

Question

[jinzheng9406]

I want to analysis a genome with PSMC

After that, I want to use samtools/bcftools/vcfutils to process the data.

And I want to follow these five rules:

(i) that read depth wasbetween 1/3 and 2-times the average coverage; (ii) that root-mean-squared mapping quality for all analyzed sites was above 10; (3) that all analyzed sites were at least 5 bp away from a predicted insertion/deletion; (4) that consensus quality was >30; (v) that at least 18 of 35 possible overlapping 35-mers in the human reference genome sequence mapped to the correct location with zero or one mismatch.

The bam file name likes genome.bai, the reference genome likes ref.fa. The samtools version may be 0.1.18 or higher.

So, how to write the command line?

Thank you!

Answer 1

[Samarth Kulshrestha]

Hi, You can follow the instructions on the given link :

http://samtools.sourceforge.net/mpileup.shtml

Well explained with all the commands for SNP/INDEL calling using SAMtools.

Best