rkwalters
commented
6 years ago Hi,
As the error states, this indicates munge_sumstats.py isn't able to find a SNP column in your input summary statistics. There's a few different common issues that could yield this error:
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The header for a required column isn't one of the recognized values. E.g. for the SNP column, which is expected to include rsids, munge_sumstats.py will recognize "snp", "markername", "snpid", "rs", "rsid", "rs_number", or "rs_numbers" (all case insensitive). If it's not one of those, you can specify what your file is using as a header for that field using the "--snp" argument.
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The file format of the summary stats isn't supported. Munge_sumstats assumes the input summary stats are whitespace delimited (after decompression) with a header row. Comma-delimited files, or other separators, or tab-delimited files that allow spaces within a field and/or indicate missing values by multiple tabs will not parse correctly.
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The summary stats are compressed using a format that isn't supported by munge_sumstats. The currently supported options are plain text, gzip (.gz), or bzip2 (.bz2), identified by the filename. If your input summary stats are compressed with a different format (e.g. .zip, as is the case for the example scz/bip files used in the tutorial on the github wiki) you'll need to decompress the file before running munge.
If none of these solve it, it would be helpful to see the full command line you're using to run munge_sumstats.py and an example of the first few rows of your input summary statistics. (Can email those separately if you're more comfortable sharing those individually rather than posting to this issues board.)
Cheers, Raymond
On Aug 31, 2018, at 10:49 AM, cmfa26 notifications@github.com wrote:
Hi, While running munge_sumstats.py, I found a error about: SNP column was not find. I following the tutorial, I did the download of all data (my_data_input and w_hm3.snplist) and software/packages, however I found this error:
Traceback (most recent call last): File "./munge_sumstats.py", line 746, in munge_sumstats(parser.parse_args(), p=True) File "./munge_sumstats.py", line 627, in munge_sumstats raise ValueError('Could not find {C} column.'.format(C=c)) ValueError: Could not find SNP column.
Could help me to figure out how to handle this kind of error?
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cmfa26
Hi,