Question: Meaning Of -A In Vcftools Vcfutils.Pl Varfilter?

0

Dan •

**520**wrote:The command line says:

```
Usage: vcfutils.pl varFilter [options] <in.vcf>
Options: -Q INT minimum RMS mapping quality for SNPs [10]
-d INT minimum read depth [2]
-D INT maximum read depth [10000000]
-a INT minimum number of alternate bases [2]
-w INT SNP within INT bp around a gap to be filtered [3]
-W INT window size for filtering adjacent gaps [10]
-1 FLOAT min P-value for strand bias (given PV4) [0.0001]
-2 FLOAT min P-value for baseQ bias [1e-100]
-3 FLOAT min P-value for mapQ bias [0]
-4 FLOAT min P-value for end distance bias [0.0001]
-e FLOAT min P-value for HWE (plus F<0) [0.0001]
-p print filtered variants
Note: Some of the filters rely on annotations generated by SAMtools/BCFtools.
```

The description of -a seems counter intuitive, why would you want two alternative alleles as the default?

Is this better written "minimum number of alternate reads supporting each alternative allele [2]"?

That would at least make sense as an option to have.

P.S. anyone know which filters rely on annotations generated by SAMtools/BCFtools?

Anyone know why -p is an option ;-)

520