#CHROM POS ID REF ALT QUAL FILTER INFO FO>
NZ_NGSV01000001 4 . G . 0 REF DP=3;RC=3;N>
NZ_NGSV01000001 5 . A . 0 REF DP=4;RC=1;N>
NZ_NGSV01000001 6 . T . 0 REF DP=9;RC=5;N>
When i run -monomorphic i thought i would get 1 line for every site.
But it excludes sites with DP=0?
Or does it only report when the length of DP=0 is > -mon_gap?
For -monomortphic it should have the DP=0 sites and give them ALT=. and GT=. (no genotype) ?
You can use . or PASS for FILTR and . for QUALITY .
When i run
-monomorphici thought i would get 1 line for every site. But it excludes sites withDP=0?Or does it only report when the length of DP=0 is > -mon_gap?
For
-monomortphicit should have the DP=0 sites and give themALT=.andGT=.(no genotype) ? You can use.orPASSforFILTRand.forQUALITY.