I think I need some ground-up assistance with filtering VCF files. I have generated a VCF file with samtools + bcftools after an initial alignment with bowtie2 and from what I can tell this VCF file looks as expected. Now I want to filter it in several ways and am struggling to figure out how to do it. The following is what I need to do:
- DP >= 10
- DP_STRAND >= 10
- QUAL >= 50
- MQ >= 30
- Not on a repetitive region
- Not less than 9nt away from a gap
Unfortunately I'm rather limited in the software I can use; I have bcftools and vcftools, as well as the ability to run any Python or Perl script, so any answers that use those would be ideal. As I'm not using my own computer I can't freely install other things, although if there's something I absolutely need I can probably ask for it.
Thanks in advance.