Hi,

I’m running the following bit of code on exome sequenced data and finding that i get different results when I plot my sample call rate after. I was wondering if the order of commands makes a difference, or if there is something else I am missing. Thanks!

```
scz = hl.read_matrix_table('Analyses/scz_main.mt')
scz = hl.sample_qc(scz, name = 'sample_qc')
scz.count_rows()
scz = scz.filter_rows(scz.alleles.length() <= 6)
scz = hl.split_multi_hts(scz, permit_shuffle=True)
scz = scz.filter_entries(
hl.is_defined(scz.GT) &
(
(scz.GT.is_hom_ref() &
(
((scz.AD[0] / scz.DP) < 0.8) |
(scz.GQ < 20) |
(scz.DP < 20)
)
) |
(scz.GT.is_het() &
(
(((scz.AD[0] + scz.AD[1]) / scz.DP) < 0.8) |
((scz.AD[1] / scz.DP) < 0.2) |
(scz.PL[0] < 20) |
(scz.DP < 20)
)
) |
(scz.GT.is_hom_var() &
(
((scz.AD[1] / scz.DP) < 0.8) |
(scz.PL[0] < 20) |
(scz.DP < 20)
)
)
),
keep = False
)
scz.count_rows()
```

I’m using hail version 0.2.36-ed011219dd93