Shapeit2 Sample Input

[boratonAJ]

I am setting up this pipeline to find local ancestry. I don't know why I am getting this error. Below is the error message.

Traceback (most recent call last): File "ancestry_pipeline/shapeit2rfmix.py", line 263, in main(args) File "ancestry_pipeline/shapeit2rfmix.py", line 131, in main sample_indices.append(find_indices(ref_set, open_shapeit(sample), out_sample)) File "ancestry_pipeline/shapeit2rfmix.py", line 46, in find_indices raise RuntimeError('Shapeit sample file appears to be incorrect') RuntimeError: Shapeit sample file appears to be incorrect

[dwuab]

I have been using this pipeline for a while and have encountered this problem before. According to the code, shapeit2rfmix.py expects the header to be

ID_1 ID_2 missing father mother sex plink_pheno

while the header of the .sample file given by shapeit2 is just

ID_1 ID_2 missing.

My workaround is to expand the .sample file to have more columns and fill in 0 wherever appropriate.

[armartin]

Apologies, as @samuelandjw indicates, just adding additional rows with 0's is a decent workaround for this plink-style file.

On May 23, 2018, at 2:49 AM, samuelandjw [email protected] wrote:

I have been using this pipeline for a while and have encountered this problem before. According to the code, shapeit2rfmix.py expects the header to be

ID_1 ID_2 missing father mother sex plink_pheno

while the header of the .sample file given by shapeit2 is just

ID_1 ID_2 missing.

My workaround is to expand the .sample file to have more columns and fill in 0 wherever appropriate.

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