Comments (7)
from polyfun.
thanks ...so those limited to uk biobank...also if I download the UK file, it seems that I need to also download related LD files and put in a directory as LDstore from here https://data.broadinstitute.org/alkesgroup/UKBB_LD/
to run_finemapper.py
--ldstore <PATH_TO_LDSTORE_EXECUTABLE>
from polyfun.
also do I need to change allele1 and 2 in uk-ld files to A1 nd A2 ( also is the A1 the effect allele -like plink- or reference allele as you wrote?)... the reason that I ask is I am getting this error:
bash-4.2$ python /usr/local/polyfun/1.0.0/run_finemapper.py --ld ldstore-uk/chr22_43000001_46000001 --sumstats 22b --n 15000 --chr 22 --start 44000000 --end 44500000 --method susie --max-num-causal 2 --out test1
- Fine-mapping Wrapper
- Version 1.0.0
- (C) 2019 Omer Weissbrod
[INFO] Loaded an LD matrix for 26498 SNPs from ldstore-uk/chr22_43000001_46000001.npz
[INFO] Loading sumstats file...
[INFO] Loaded sumstats for 99 SNPs
Traceback (most recent call last):
File "/usr/local/anaconda3/envs/polyfun/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 2646, in get_loc
return self._engine.get_loc(key)
File "pandas/_libs/index.pyx", line 111, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 1618, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 1626, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'A1'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/polyfun/1.0.0/run_finemapper.py", line 123, in
verbose=args.verbose, ld=ld, df_ld_snps=df_ld_snps, debug_dir=args.debug_dir)
File "/usr/local/polyfun/1.0.0/finemapper.py", line 388, in finemap
self.sync_ld_sumstats(ld, df_ld_snps)
File "/usr/local/polyfun/1.0.0/finemapper.py", line 121, in sync_ld_sumstats
df_ld_snps = set_snpid_index(df_ld_snps)
File "/usr/local/polyfun/1.0.0/finemapper.py", line 18, in set_snpid_index
df['A1_first'] = (df['A1'] < df['A2']) | (df['A1'].str.len()>1) | (df['A2'].str.len()>1)
File "/usr/local/anaconda3/envs/polyfun/lib/python3.6/site-packages/pandas/core/frame.py", line 2800, in getitem
indexer = self.columns.get_loc(key)
File "/usr/local/anaconda3/envs/polyfun/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 2648, in get_loc
return self._engine.get_loc(self._maybe_cast_indexer(key))
File "pandas/_libs/index.pyx", line 111, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 1618, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 1626, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'A1'
from polyfun.
from polyfun.
thank you for the info. so my sumstat file has A1 and A2 but the uk-LD file that I downloaded from ukbiobank (https://data.broadinstitute.org/alkesgroup/UKBB_LD/) has allele1 and allele2 in header as well as rsid (instead of SNP). not sure if the above error might be related to these headers and if yes, do I need to change the header in uk files to A1 and A2. I can decompress the gz file to do that but not sure about npz file.
thanks
from polyfun.
from polyfun.
from polyfun.
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from polyfun.