Predict.py with imputation data

[Hannah430]

Hi,

I have been trying to run PrediXcan using imputed data (by TopMED). however, the program has been running for many days, and I am wondering if it is normal and whether I did something wrong.

The imputed data is already in hg38 build. and here's an example of of input: chr21:10017726:G:A

Here is the script: python3 ./Predict.py \ --model_db_path $MODEL/mashr_Brain_Frontal_Cortex_BA9.db \ --model_db_snp_key varID \ --vcf_genotypes $DATA/chr*.clean.noMono.vcf.gz \ --vcf_mode imputed \ --on_the_flymapping METADATA "{}{}{}{}_b38" \ --prediction_output $RESULTS/predict.txt \ --prediction_summary_output $RESULTS/predict_summary.txt \ --verbosity 9 \ --throw

I am also wondering if there's a way to see how many SNPs have been used by the PrediXcan model? I did a trial run with data fro one chromosome, and the _summary.txt shows "NA" for the majority of the predicted gene.

Thank you! Hannah

[Fnyasimi]

Running for many days is already an issue, kindly check out if there is an issue on the log. Ideally it should take a short time to run and the software reports the % of the model's SNPs used for prediction

[Hannah430]

Hi,

So far, the log just says that it is processing the vcf files. I'm wondering if it is okay to input genotype data in many files according to chromosome number. Also I am also wondering if the --on_the_fly_mapping METADATA "{}_{}_{}_{}_b38 is correct for my case (an example of my input: chr21:10017726:G:A).

thank you! Hannah

[Fnyasimi]

You can input the genotype files for each chromosome using a wild card as you have done with your code above. You can use on the fly mapping argument to reconstruct the varID from the respective columns in the vcf file

[Hannah430]

Hi,

I have tried your suggestions, and still hasn't fix the issue of the lengthy running time. I am wondering if it's normal, but how can I fix it if it's not normal.

also while running the program, there is a message indicating that the index file is older than the data file. I am wondering if this will cause a problem?

Thank you! Hannah