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I went through the manuals and can't find the meaning of the below flag:

-filt_rules_l 'filter==0'

Here is the link to manual for this flag: filt_rules_l

Can anyone explain?

IMPUTE version:

impute_v2.3.1_x86_64_dynamic

Edit: The full IMPUTE2 code is irrelevant, I am not using the command to impute, I received an imputed data and the script used to impute. This one flag was a mystery to me. I will update the post with impute software version when I find out.

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I have never used this program, but reading the manual in the link it has to mean the following.

The manual says:

Writing -filt_rules_l 'eur.maf<0.05' on the command line would tell the program to remove any variants with eur.maf values less than 0.05 from the reference panel.

So, -filt_rules_l 'filter==0' would mean that the program removes any variants with filter values of 0 from the reference panel. In the legend file there should be a column named filter, which are filtered out when the value is 0.

Here is the example legend file, in your case there must be a custom additional column named "filter":

$ head ALL_1000G_phase1integrated_v3_chr1_impute.legend

id position a0 a1 afr.aaf amr.aaf asn.aaf eur.aaf afr.maf amr.maf asn.maf eur.maf
rs58108140 10583 G A 0.0407 0.1713 0.1311 0.2071 0.0407 0.1713 0.1311 0.2071
rs189107123 10611 C G 0.0142 0.0276 0.0140 0.0211 0.0142 0.0276 0.0140 0.0211
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  • $\begingroup$ Thank you, are you suggesting that reference panel has column named "filter"? I will have to check. But I think "eur.maf" column is calculated on the fly from the reference file, need to check. $\endgroup$
    – zx8754
    Nov 17 '17 at 10:48
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    $\begingroup$ If you want to use your command it should. If not it won't work, and you need to find the column on which you want to filter. $\endgroup$
    – benn
    Nov 17 '17 at 10:55
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    $\begingroup$ Yes, sorry I have missed the _l bit, meaning this filter works from legend file, which in my case apparently had a modified version of Phase3 legend file with extra "filter" column. All makes sense now. Thank you. $\endgroup$
    – zx8754
    Nov 20 '17 at 9:15

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