I have a set of illumina paired end reads (rone.fq and rtwo.fq), and I have mapped those reads to a reference (ref.fa).
Now I am trying to get SNP and INDEL information using the following script
I get the following VCF (this is just one line of the VCF I actually get)
I am assuming that samtools thinks this is a SNP, because the REF=A and ALT=C,X. My question is: How can I know the coverage depth of this SNP given this VCF? If this VCF does not have information enough to show the SNP coverage depth then how can I creat a VCF that shows that information? Thanks
asked 21 May '12, 17:12
right from the VCF spec:
Samtools depth reports raw coverage. In the VCF file DP reports the coverage of all reads at that loci (that pass the quality filter). So 'Samtools depth' gives a different statistics than the DP field.
There is also information about the depth on each strand supporting the ref / alt.
IT is worth your time to carefully read the documentation for all the Samtools steps