Different format of snp for Knight(WashU) genotype data

[zq2209]

When running cis for Knight data, I am getting the error.

Traceback (most recent call last):
File "/home/zq2209/.sos/e0257c72c6594a84/singularity_run_4940.py", line 61, in
pairs_df = pairs_df.assign(
File "/opt/conda/lib/python3.8/site-packages/pandas/core/frame.py", line 3827, in assign
data[k] = com.apply_if_callable(v, data)
File "/opt/conda/lib/python3.8/site-packages/pandas/core/common.py", line 329, in apply_if_callable
return maybe_callable(obj, **kwargs)
File "/home/zq2209/.sos/e0257c72c6594a84/singularity_run_4940.py", line 63, in
ref = lambda dataframe: dataframe['variant_id'].map(lambda variant_id:variant_id.split("_")[-2])).assign(
File "/opt/conda/lib/python3.8/site-packages/pandas/core/series.py", line 3879, in map
new_values = super()._map_values(arg, na_action=na_action)
File "/opt/conda/lib/python3.8/site-packages/pandas/core/base.py", line 937, in _map_values
new_values = map_f(values, mapper)
File "pandas/_libs/lib.pyx", line 2467, in pandas.libs.lib.map_infer
File "/home/zq2209/.sos/e0257c72c6594a84/singularity_run_4940.py", line 63, in
ref = lambda dataframe: dataframe['variant_id'].map(lambda variant_id:variant_id.split("")[-2])).assign(
IndexError: list index out of range

After running line by line, this is because snp column in Knight genotype file has a different format compared to ROSMAP genotype data.

In ROSMAP, the format of snp is likechr1:248945797_G_C, but in Knight, it is chr1:732994:G:A. Knight use : instead of _. Details shown in attached screenshots. This cause the pipeline return that index error.

Two possible solutions:

1. Munually change the format of snp in Knight genotype file.
2. Incorporate some changes in our qc_no_prune in the GWAS_QC pipeline.

I will use 1 for now. And I will make some changes to pipeline later.

[hsun3163]

@zq2209 Actually, sorry, I didn't realize last night that the mechanism necessary to fix both the FID and the SNP names are all in the qc_no_prune already. Instead of changing them, can you try to do item 1 via the qc_no_prune command?

[zq2209]

I have tried qc_no_prune for Knight. It have solved the SNP name. But the FID was not solved. Should we incorporate some changes to deal with FID?