Entering edit mode

7 days ago

bandanaschapagain
▴
30

Hi, I am using samtools inbuilt https://github.com/lh3/samtools/blob/master/bcftools/vcfutils.pl to filter my vcf file. So before setting up my parameters, I wanted to know what is the default value set in the script for these options:

Options:

-Q INT minimum RMS mapping quality for SNPs [$opts{Q}]

```
-d INT minimum read depth [$opts{d}]
-D INT maximum read depth [$opts{D}]
-a INT minimum number of alternate bases [$opts{a}]
-w INT SNP within INT bp around a gap to be filtered [$opts{w}]
-W INT window size for filtering adjacent gaps [$opts{W}]
-1 FLOAT min P-value for strand bias (given PV4) [$opts{1}]
-2 FLOAT min P-value for baseQ bias [$opts{2}]
-3 FLOAT min P-value for mapQ bias [$opts{3}]
-4 FLOAT min P-value for end distance bias [$opts{4}]
-e FLOAT min P-value for HWE (plus F<0) [$opts{e}]
-p print filtered variants
```

Thank you!