Problem with missing freq column

[chenming9453]

Hi all,

My summary data lacked the maf column. When I tried to run mtag. I got the following error:

Traceback (most recent call last):
File "/ysm-gpfs/pi/zhao/mc2792/software/mtag/mtag.py", line 1567, in
mtag(args)
File "/ysm-gpfs/pi/zhao/mc2792/software/mtag/mtag.py", line 1336, in mtag
DATA_U, DATA, args = load_and_merge_data(args)
File "/ysm-gpfs/pi/zhao/mc2792/software/mtag/mtag.py", line 294, in load_and_merge_data
raise IOError("--maf_min is specified but maf column is not present in sumstats {}".format(p+1))
IOError: --maf_min is specified but maf column is not present in sumstats 2

I am wondering if the maf column is necessary for mtag? I did not find any flag to avoid using maf.

Best,
Ming

[paturley]

MTAG does require the MAF column, but you can use allele frequencies from a reference panel if you'd like.

…

On Sun, Nov 17, 2019 at 10:00 PM chenming9453 ***@***.***> wrote: Hi all, My summary data lacked the maf column. When I tried to run mtag. I got the following error: Traceback (most recent call last): File "/ysm-gpfs/pi/zhao/mc2792/software/mtag/mtag.py", line 1567, in mtag(args) File "/ysm-gpfs/pi/zhao/mc2792/software/mtag/mtag.py", line 1336, in mtag DATA_U, DATA, args = load_and_merge_data(args) File "/ysm-gpfs/pi/zhao/mc2792/software/mtag/mtag.py", line 294, in load_and_merge_data raise IOError("--maf_min is specified but maf column is not present in sumstats {}".format(p+1)) IOError: --maf_min is specified but maf column is not present in sumstats 2 I am wondering if the maf column is necessary for mtag? I did not find any flag to avoid using maf. Best, Ming — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#83>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFBUB5PMCYV72M25CFUTRL3QUIAMRANCNFSM4JONMQYA> .

[chenming9453]

Thank you for your prompt response! And Thank you for the solution.

Best,
Ming

[divbru]

Hi, does the --eaf_name require MAF or the effect allele (a1) frequency ?
The tutorial refers to EAF while the manual (./mtag.py -h) refers to the MAF. Thank you!

[paturley]

Ah! Thanks for catching the discrepancy. It should be the effect allele frequency.

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On Tue, Mar 7, 2023 at 2:38 AM Divya ***@***.***> wrote: Hi, does the --eaf_name require MAF or the effect allele (a1) frequency ? The tutorial refers to EAF while the manual (./mtag.py -h) refers to the MAF. Thank you! — Reply to this email directly, view it on GitHub <#83 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFBUB5LU23KX3CBCHAUSDTLW23QV5ANCNFSM4JONMQYA> . You are receiving this because you commented.Message ID: ***@***.***>